This is the pathway enrichment analysis practical of the OBDS course
The first part of this pracical is using gprofiler to perform ORA on output dataset of differentially expressed genes from DESeq2
The major aim of this exercise is to get you used to reading online tool documentation and playing with different paramters.
# load librarys
library(tidyverse)## Warning: package 'tidyverse' was built under R version 4.2.2## -- Attaching packages --------------------------------------- tidyverse 1.3.2 --
## v ggplot2 3.4.0 v purrr 0.3.5
## v tibble 3.1.8 v dplyr 1.0.10
## v tidyr 1.2.1 v stringr 1.4.1
## v readr 2.1.3 v forcats 0.5.2## Warning: package 'ggplot2' was built under R version 4.2.2## Warning: package 'tibble' was built under R version 4.2.2## Warning: package 'tidyr' was built under R version 4.2.2## Warning: package 'readr' was built under R version 4.2.2## Warning: package 'purrr' was built under R version 4.2.2## Warning: package 'dplyr' was built under R version 4.2.2## Warning: package 'stringr' was built under R version 4.2.2## Warning: package 'forcats' was built under R version 4.2.2## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()library(gprofiler2)## Warning: package 'gprofiler2' was built under R version 4.2.2# read in results table we output from DESeq2 this morning using tidyverse read_csv()
all_genes_df <- read_csv("CD8_vs_CD4_DE_results_lfcshrinkage.csv")## Rows: 22535 Columns: 9
## -- Column specification --------------------------------------------------------
## Delimiter: ","
## chr (3): ensembl_gene_ids, mgi_symbols, gene_symbols
## dbl (6): baseMean, log2FoldChange, lfcSE, pvalue, padj, ENTREZ_IDs
##
## i Use `spec()` to retrieve the full column specification for this data.
## i Specify the column types or set `show_col_types = FALSE` to quiet this message.# check its dimensions - and look at the top of the file -> what does this tell us about our table?
dim(all_genes_df)## [1] 22535 9# dim = 22,535 -> this contains all genes -> need to filter to get those tested We want to perform a classic Over representation analsis (ORA) using gprofiler - to do this we first need to create our gene subsets
# Subset 1 - All genes tested in differential expression (this is our background/control gene list) - i.e. remove padj == NA
head(all_genes_df)## # A tibble: 6 x 9
## ensembl_gen~1 baseM~2 log2Fo~3 lfcSE pvalue padj mgi_s~4 gene_~5 ENTRE~6
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr> <dbl>
## 1 ENSMUSG00000~ 1.65e-1 -2.43e-2 0.601 8.54e-1 NA MGI:MG~ Rp1 19888
## 2 ENSMUSG00000~ 3.36e-1 -7.34e-4 0.599 9.73e-1 NA MGI:MG~ Sox17 20671
## 3 ENSMUSG00000~ 4.78e+2 2.61e-1 0.118 2.42e-2 0.0603 <NA> <NA> NA
## 4 ENSMUSG00000~ 6.90e+2 1.56e-1 0.101 1.16e-1 0.225 MGI:MG~ Mrpl15 27395
## 5 ENSMUSG00000~ 3.00e+3 2.16e-1 0.0651 8.37e-4 0.00303 MGI:MG~ Lypla1 18777
## 6 ENSMUSG00000~ 8.89e+2 -5.33e-2 0.0946 5.70e-1 0.729 MGI:MG~ Tcea1 21399
## # ... with abbreviated variable names 1: ensembl_gene_ids, 2: baseMean,
## # 3: log2FoldChange, 4: mgi_symbols, 5: gene_symbols, 6: ENTREZ_IDsall_genes_tested_df <- all_genes_df[!is.na(all_genes_df$padj), ]
all_genes_tested_df## # A tibble: 17,729 x 9
## ensembl_gene~1 baseM~2 log2F~3 lfcSE pvalue padj mgi_s~4 gene_~5 ENTRE~6
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr> <dbl>
## 1 ENSMUSG000000~ 478. 0.261 0.118 2.42e-2 6.03e-2 <NA> <NA> NA
## 2 ENSMUSG000000~ 690. 0.156 0.101 1.16e-1 2.25e-1 MGI:MG~ Mrpl15 27395
## 3 ENSMUSG000000~ 3003. 0.216 0.0651 8.37e-4 3.03e-3 MGI:MG~ Lypla1 18777
## 4 ENSMUSG000000~ 889. -0.0533 0.0946 5.70e-1 7.29e-1 MGI:MG~ Tcea1 21399
## 5 ENSMUSG000000~ 18.4 0.274 0.445 3.86e-1 5.60e-1 <NA> <NA> NA
## 6 ENSMUSG000000~ 1106. 0.198 0.0890 2.46e-2 6.13e-2 MGI:MG~ Atp6v1h 108664
## 7 ENSMUSG000000~ 1.78 -0.136 0.609 2.43e-1 4.00e-1 MGI:MG~ Oprk1 18387
## 8 ENSMUSG000000~ 3436. 0.0296 0.0655 6.65e-1 8.01e-1 MGI:MG~ Rb1cc1 12421
## 9 ENSMUSG000000~ 28.3 -0.173 0.379 5.56e-1 7.17e-1 <NA> <NA> NA
## 10 ENSMUSG000000~ 1539. -0.468 0.0789 2.01e-9 1.59e-8 MGI:MG~ Pcmtd1 319263
## # ... with 17,719 more rows, and abbreviated variable names
## # 1: ensembl_gene_ids, 2: baseMean, 3: log2FoldChange, 4: mgi_symbols,
## # 5: gene_symbols, 6: ENTREZ_IDs# Subset 2 - All sig upregulated genes (padj < 0.05. & log2FoldChange > 1)
upreg_genes_df <- all_genes_df [all_genes_df$padj < 0.05 & all_genes_df$log2FoldChange > 1, ]
upreg_genes_df## # A tibble: 915 x 9
## ensembl_gen~1 baseM~2 log2F~3 lfcSE pvalue padj mgi_s~4 gene_~5 ENTRE~6
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr> <dbl>
## 1 ENSMUSG00000~ 23.6 1.66 0.572 3.65e- 4 1.42e- 3 MGI:MG~ Slco5a1 240726
## 2 ENSMUSG00000~ 196. 2.20 0.200 3.15e-29 7.26e-28 MGI:MG~ Ogfrl1 70155
## 3 ENSMUSG00000~ 344. 2.82 0.159 6.72e-72 4.27e-70 MGI:MG~ Tbc1d8 54610
## 4 ENSMUSG00000~ 603. 1.84 0.116 1.51e-57 7.74e-56 MGI:MG~ Fhl2 14200
## 5 ENSMUSG00000~ 362. 1.28 0.139 1.10e-20 1.82e-19 MGI:MG~ Nrp2 18187
## 6 ENSMUSG00000~ 198. 1.98 0.196 3.74e-25 7.52e-24 MGI:MG~ Adam23 23792
## 7 ENSMUSG00000~ 17.7 3.07 0.746 2.73e- 6 1.51e- 5 MGI:MG~ Fn1 14268
## 8 ENSMUSG00000~ 6.22 3.26 1.50 2.11e- 3 7.03e- 3 MGI:MG~ Cxcr2 12765
## 9 ENSMUSG00000~ 47.1 2.22 0.413 6.51e- 9 4.90e- 8 MGI:MG~ Slc11a1 18173
## 10 ENSMUSG00000~ 136. 2.79 0.250 5.38e-30 1.28e-28 MGI:MG~ Cyp27a1 104086
## # ... with 905 more rows, and abbreviated variable names 1: ensembl_gene_ids,
## # 2: baseMean, 3: log2FoldChange, 4: mgi_symbols, 5: gene_symbols,
## # 6: ENTREZ_IDsdim(upreg_genes_df)## [1] 915 9# Subset 3 - All sig downregulated genes (padj < 0.05. & log2FoldChange < 1)
downreg_genes_df <- all_genes_df [all_genes_df$padj < 0.05 & all_genes_df$log2FoldChange < -1, ]
downreg_genes_df## # A tibble: 1,204 x 9
## ensembl_~1 baseM~2 log2F~3 lfcSE pvalue padj mgi_s~4 gene_~5 ENTRE~6
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <chr> <dbl>
## 1 ENSMUSG00~ 89.6 -1.10 0.274 1.32e- 5 6.64e- 5 MGI:MG~ Paqr8 7.42e4
## 2 ENSMUSG00~ 116. -1.76 0.249 1.92e- 13 2.10e- 12 MGI:MG~ Kcnq5 2.27e5
## 3 ENSMUSG00~ 98.2 -2.47 0.289 9.86e- 19 1.48e- 17 MGI:MG~ Fam135a 6.82e4
## 4 ENSMUSG00~ 32.2 -1.60 0.490 1.07e- 4 4.63e- 4 MGI:MG~ Bend6 3.21e5
## 5 ENSMUSG00~ 1059. -4.15 0.115 8.49e-284 3.01e-281 MGI:MG~ Dst 1.35e4
## 6 ENSMUSG00~ 1507. -1.52 0.0794 3.50e- 82 2.64e- 80 MGI:MG~ Aff3 1.68e4
## 7 ENSMUSG00~ 16.2 -2.29 0.773 1.82e- 4 7.54e- 4 MGI:MG~ Npas2 1.81e4
## 8 ENSMUSG00~ 5.74 -3.03 1.72 3.01e- 3 9.69e- 3 MGI:MG~ Gm16894 1.00e8
## 9 ENSMUSG00~ 60.7 -3.54 0.421 3.26e- 18 4.78e- 17 MGI:MG~ Il1r1 1.62e4
## 10 ENSMUSG00~ 137. -1.02 0.222 1.19e- 6 6.91e- 6 MGI:MG~ Il1rl2 1.08e5
## # ... with 1,194 more rows, and abbreviated variable names 1: ensembl_gene_ids,
## # 2: baseMean, 3: log2FoldChange, 4: mgi_symbols, 5: gene_symbols,
## # 6: ENTREZ_IDsdim(downreg_genes_df)## [1] 1204 9# Check the dimensions of each of your dataframes using dim()
# all_genes_df_filtered should be 17729
# upreg_genes_df should be 915
# downreg_genes_df should be 1204# from each of these dataframes get a vector of the ensembl ids
all_gene_ids <- all_genes_df$ensembl_gene_ids
upreg_gene_ids <-upreg_genes_df$ensembl_gene_ids
downreg_gene_ids <- downreg_genes_df$ensembl_gene_ids#Perform ORA using g:profiler
# use the gost() function - what parameters should we include/change??
# we want to test the ORA of upreg_gene_ids vs our all_gene_ids
# get help for function
?gost() ## starting httpd help server ... done# write query and assign to output variable named `gost_results_obj`
gost_results_obj <- gost(query = upreg_gene_ids, organism = "mmusculus",exclude_iea = TRUE,correction_method = "g_SCS",custom_bg = all_gene_ids)## Detected custom background input, domain scope is set to 'custom'gost_results_obj$result## query significant p_value term_size query_size intersection_size
## 1 query_1 TRUE 2.107197e-03 3 910 3
## 2 query_1 TRUE 8.162242e-03 4 910 3
## 3 query_1 TRUE 4.992293e-02 2 910 2
## 4 query_1 TRUE 6.064566e-100 1293 910 255
## 5 query_1 TRUE 1.423457e-99 2195 910 330
## 6 query_1 TRUE 5.069491e-64 6166 910 508
## 7 query_1 TRUE 1.399244e-63 140 910 77
## 8 query_1 TRUE 4.659060e-59 407 910 116
## 9 query_1 TRUE 1.162991e-56 1209 910 193
## 10 query_1 TRUE 5.249905e-56 552 910 130
## 11 query_1 TRUE 5.706629e-56 275 910 95
## 12 query_1 TRUE 6.230068e-56 282 910 96
## 13 query_1 TRUE 8.371692e-56 276 910 95
## 14 query_1 TRUE 2.163717e-54 784 910 152
## 15 query_1 TRUE 7.062562e-54 425 910 113
## 16 query_1 TRUE 1.393829e-52 916 910 162
## 17 query_1 TRUE 1.513074e-52 1111 910 179
## 18 query_1 TRUE 1.998810e-52 1113 910 179
## 19 query_1 TRUE 3.888858e-52 602 910 131
## 20 query_1 TRUE 7.687026e-52 1006 910 169
## 21 query_1 TRUE 1.589598e-51 1140 910 180
## 22 query_1 TRUE 1.635668e-51 1225 910 187
## 23 query_1 TRUE 3.386643e-51 2078 910 250
## 24 query_1 TRUE 1.014386e-49 339 910 98
## 25 query_1 TRUE 4.550835e-49 857 910 152
## 26 query_1 TRUE 1.155217e-48 324 910 95
## 27 query_1 TRUE 1.429990e-48 528 910 119
## 28 query_1 TRUE 4.045675e-48 773 910 143
## 29 query_1 TRUE 4.936322e-48 242 910 83
## 30 query_1 TRUE 4.573130e-47 1848 910 227
## 31 query_1 TRUE 7.552616e-47 780 910 142
## 32 query_1 TRUE 7.763299e-47 145 910 66
## 33 query_1 TRUE 1.172027e-46 1303 910 186
## 34 query_1 TRUE 3.190003e-46 153 910 67
## 35 query_1 TRUE 3.436175e-46 117 910 60
## 36 query_1 TRUE 6.788926e-46 104 910 57
## 37 query_1 TRUE 5.586787e-45 276 910 85
## 38 query_1 TRUE 6.214854e-45 618 910 124
## 39 query_1 TRUE 6.894623e-45 3860 910 348
## 40 query_1 TRUE 7.194380e-45 159 910 67
## 41 query_1 TRUE 3.161976e-44 637 910 125
## 42 query_1 TRUE 5.862704e-44 661 910 127
## 43 query_1 TRUE 2.075747e-43 117 910 58
## 44 query_1 TRUE 8.307551e-43 331 910 90
## 45 query_1 TRUE 2.515264e-42 216 910 74
## 46 query_1 TRUE 6.829537e-42 372 910 94
## 47 query_1 TRUE 1.517391e-41 124 910 58
## 48 query_1 TRUE 1.971915e-41 4265 910 363
## 49 query_1 TRUE 2.469516e-41 533 910 111
## 50 query_1 TRUE 4.421286e-41 282 910 82
## 51 query_1 TRUE 1.106968e-40 4314 910 364
## 52 query_1 TRUE 6.469746e-40 2108 910 232
## 53 query_1 TRUE 9.301965e-40 428 910 98
## 54 query_1 TRUE 3.300858e-39 443 910 99
## 55 query_1 TRUE 3.855096e-39 3165 910 296
## 56 query_1 TRUE 8.407565e-39 341 910 87
## 57 query_1 TRUE 1.041185e-37 197 910 67
## 58 query_1 TRUE 1.716478e-37 172 910 63
## 59 query_1 TRUE 2.921060e-37 193 910 66
## 60 query_1 TRUE 3.192367e-37 382 910 90
## 61 query_1 TRUE 3.595537e-36 221 910 69
## 62 query_1 TRUE 2.268158e-32 204 910 63
## 63 query_1 TRUE 2.059199e-31 5099 910 383
## 64 query_1 TRUE 4.668333e-31 5117 910 383
## 65 query_1 TRUE 4.827052e-31 2954 910 266
## 66 query_1 TRUE 1.771609e-28 496 910 91
## 67 query_1 TRUE 1.810591e-27 4597 910 347
## 68 query_1 TRUE 9.675813e-27 8847 910 545
## 69 query_1 TRUE 2.034788e-24 8408 910 519
## 70 query_1 TRUE 4.186015e-24 14827 910 770
## 71 query_1 TRUE 8.975356e-19 7956 910 481
## 72 query_1 TRUE 1.618933e-17 1257 910 131
## 73 query_1 TRUE 1.055415e-15 1241 910 126
## 74 query_1 TRUE 5.267631e-15 726 910 89
## 75 query_1 TRUE 6.755757e-14 1368 910 130
## 76 query_1 TRUE 2.933808e-13 3398 910 243
## 77 query_1 TRUE 6.373505e-13 796 910 90
## 78 query_1 TRUE 7.964155e-13 2331 910 184
## 79 query_1 TRUE 1.867338e-12 781 910 88
## 80 query_1 TRUE 2.852995e-12 540 910 70
## 81 query_1 TRUE 3.981608e-12 216 910 42
## 82 query_1 TRUE 6.362281e-12 5231 910 330
## 83 query_1 TRUE 3.828121e-11 388 910 56
## 84 query_1 TRUE 4.794349e-11 1081 910 105
## 85 query_1 TRUE 4.856609e-11 1320 910 120
## 86 query_1 TRUE 1.021625e-10 1000 910 99
## 87 query_1 TRUE 1.090293e-10 3199 910 224
## 88 query_1 TRUE 1.582653e-10 340 910 51
## 89 query_1 TRUE 1.891685e-10 3292 910 228
## 90 query_1 TRUE 3.727571e-10 3177 910 221
## 91 query_1 TRUE 4.167784e-10 3432 910 234
## 92 query_1 TRUE 5.629797e-10 258 910 43
## 93 query_1 TRUE 5.845589e-10 874 910 89
## 94 query_1 TRUE 6.322663e-10 11697 910 606
## 95 query_1 TRUE 7.251044e-10 317 910 48
## 96 query_1 TRUE 7.385458e-10 238 910 41
## 97 query_1 TRUE 8.512241e-10 2744 910 197
## 98 query_1 TRUE 1.017640e-09 837 910 86
## 99 query_1 TRUE 1.250448e-09 4405 910 281
## 100 query_1 TRUE 1.272388e-09 2092 910 161
## 101 query_1 TRUE 2.779068e-09 154 910 32
## 102 query_1 TRUE 2.885352e-09 929 910 91
## 103 query_1 TRUE 3.766984e-09 206 910 37
## 104 query_1 TRUE 5.908131e-09 188 910 35
## 105 query_1 TRUE 7.535138e-09 532 910 63
## 106 query_1 TRUE 7.693616e-09 2173 910 163
## 107 query_1 TRUE 8.809356e-09 3786 910 247
## 108 query_1 TRUE 1.068354e-08 2969 910 205
## 109 query_1 TRUE 1.091120e-08 1240 910 109
## 110 query_1 TRUE 1.660789e-08 249 910 40
## 111 query_1 TRUE 1.821200e-08 195 910 35
## 112 query_1 TRUE 1.867337e-08 1435 910 120
## 113 query_1 TRUE 2.044474e-08 462 910 57
## 114 query_1 TRUE 2.239343e-08 463 910 57
## 115 query_1 TRUE 2.246938e-08 545 910 63
## 116 query_1 TRUE 2.369455e-08 1440 910 120
## 117 query_1 TRUE 2.454454e-08 1913 910 147
## 118 query_1 TRUE 2.626632e-08 2297 910 168
## 119 query_1 TRUE 2.726149e-08 647 910 70
## 120 query_1 TRUE 4.166272e-08 2291 910 167
## 121 query_1 TRUE 4.270955e-08 15 910 11
## 122 query_1 TRUE 4.517875e-08 4908 910 299
## 123 query_1 TRUE 5.338083e-08 12 910 10
## 124 query_1 TRUE 5.338083e-08 12 910 10
## 125 query_1 TRUE 5.338083e-08 12 910 10
## 126 query_1 TRUE 6.074301e-08 4732 910 290
## 127 query_1 TRUE 6.381586e-08 65 910 20
## 128 query_1 TRUE 7.318475e-08 97 910 24
## 129 query_1 TRUE 1.255354e-07 108 910 25
## 130 query_1 TRUE 1.314378e-07 16 910 11
## 131 query_1 TRUE 1.336163e-07 242 910 38
## 132 query_1 TRUE 1.479151e-07 641 910 68
## 133 query_1 TRUE 1.966603e-07 245 910 38
## 134 query_1 TRUE 2.275773e-07 4001 910 252
## 135 query_1 TRUE 2.402435e-07 575 910 63
## 136 query_1 TRUE 2.984931e-07 2346 910 167
## 137 query_1 TRUE 3.275154e-07 399 910 50
## 138 query_1 TRUE 3.477569e-07 49 910 17
## 139 query_1 TRUE 3.681953e-07 2655 910 183
## 140 query_1 TRUE 4.175980e-07 251 910 38
## 141 query_1 TRUE 4.285843e-07 671 910 69
## 142 query_1 TRUE 4.883894e-07 658 910 68
## 143 query_1 TRUE 5.285144e-07 2647 910 182
## 144 query_1 TRUE 5.298578e-07 486 910 56
## 145 query_1 TRUE 5.336842e-07 253 910 38
## 146 query_1 TRUE 1.000697e-06 5054 910 300
## 147 query_1 TRUE 1.041772e-06 52 910 17
## 148 query_1 TRUE 1.314862e-06 1373 910 111
## 149 query_1 TRUE 1.794026e-06 785 910 75
## 150 query_1 TRUE 2.048944e-06 77 910 20
## 151 query_1 TRUE 3.825641e-06 88 910 21
## 152 query_1 TRUE 3.998775e-06 862 910 79
## 153 query_1 TRUE 4.154208e-06 49 910 16
## 154 query_1 TRUE 4.315766e-06 116 910 24
## 155 query_1 TRUE 6.079918e-06 312 910 41
## 156 query_1 TRUE 6.502443e-06 128 910 25
## 157 query_1 TRUE 6.975241e-06 563 910 59
## 158 query_1 TRUE 7.357867e-06 825 910 76
## 159 query_1 TRUE 8.006582e-06 66 910 18
## 160 query_1 TRUE 8.029677e-06 240 910 35
## 161 query_1 TRUE 9.595034e-06 424 910 49
## 162 query_1 TRUE 1.051306e-05 1617 910 122
## 163 query_1 TRUE 1.051907e-05 67 910 18
## 164 query_1 TRUE 1.232314e-05 2925 910 191
## 165 query_1 TRUE 1.295856e-05 132 910 25
## 166 query_1 TRUE 1.439032e-05 443 910 50
## 167 query_1 TRUE 1.497747e-05 589 910 60
## 168 query_1 TRUE 1.760259e-05 474 910 52
## 169 query_1 TRUE 1.816154e-05 155 910 27
## 170 query_1 TRUE 1.977497e-05 519 910 55
## 171 query_1 TRUE 2.047836e-05 1420 910 110
## 172 query_1 TRUE 2.739782e-05 423 910 48
## 173 query_1 TRUE 2.739782e-05 423 910 48
## 174 query_1 TRUE 3.083665e-05 277 910 37
## 175 query_1 TRUE 3.535927e-05 870 910 77
## 176 query_1 TRUE 4.058160e-05 64 910 17
## 177 query_1 TRUE 4.110309e-05 792 910 72
## 178 query_1 TRUE 4.196187e-05 713 910 67
## 179 query_1 TRUE 5.039914e-05 162 910 27
## 180 query_1 TRUE 5.225714e-05 82 910 19
## 181 query_1 TRUE 5.652957e-05 283 910 37
## 182 query_1 TRUE 5.959046e-05 36 910 13
## 183 query_1 TRUE 6.202702e-05 704 910 66
## 184 query_1 TRUE 6.511430e-05 83 910 19
## 185 query_1 TRUE 7.090772e-05 379 910 44
## 186 query_1 TRUE 7.137813e-05 464 910 50
## 187 query_1 TRUE 8.584483e-05 103 910 21
## 188 query_1 TRUE 8.794177e-05 1674 910 122
## 189 query_1 TRUE 9.178647e-05 301 910 38
## 190 query_1 TRUE 9.342094e-05 1281 910 100
## 191 query_1 TRUE 9.904444e-05 454 910 49
## 192 query_1 TRUE 1.033366e-04 104 910 21
## 193 query_1 TRUE 1.057630e-04 251 910 34
## 194 query_1 TRUE 1.103847e-04 470 910 50
## 195 query_1 TRUE 1.290736e-04 38 910 13
## 196 query_1 TRUE 1.323955e-04 216 910 31
## 197 query_1 TRUE 1.341075e-04 266 910 35
## 198 query_1 TRUE 1.427915e-04 1169 910 93
## 199 query_1 TRUE 1.488493e-04 293 910 37
## 200 query_1 TRUE 1.559498e-04 159 910 26
## 201 query_1 TRUE 1.587312e-04 1294 910 100
## 202 query_1 TRUE 1.824437e-04 349 910 41
## 203 query_1 TRUE 1.913389e-04 756 910 68
## 204 query_1 TRUE 2.021125e-04 392 910 44
## 205 query_1 TRUE 2.021125e-04 392 910 44
## 206 query_1 TRUE 2.063008e-04 615 910 59
## 207 query_1 TRUE 2.077398e-04 220 910 31
## 208 query_1 TRUE 2.553603e-04 395 910 44
## 209 query_1 TRUE 2.580351e-04 1218 910 95
## 210 query_1 TRUE 2.706178e-04 468 910 49
## 211 query_1 TRUE 2.722672e-04 1523 910 112
## 212 query_1 TRUE 3.174782e-04 153 910 25
## 213 query_1 TRUE 3.538123e-04 34 910 12
## 214 query_1 TRUE 3.543292e-04 56 910 15
## 215 query_1 TRUE 3.869065e-04 488 910 50
## 216 query_1 TRUE 3.957219e-04 9 910 7
## 217 query_1 TRUE 4.036715e-04 1867 910 130
## 218 query_1 TRUE 5.060270e-04 1217 910 94
## 219 query_1 TRUE 5.133792e-04 168 910 26
## 220 query_1 TRUE 5.832390e-04 910 910 76
## 221 query_1 TRUE 6.140164e-04 378 910 42
## 222 query_1 TRUE 6.146293e-04 510 910 51
## 223 query_1 TRUE 6.311133e-04 125 910 22
## 224 query_1 TRUE 8.040528e-04 484 910 49
## 225 query_1 TRUE 9.300886e-04 209 910 29
## 226 query_1 TRUE 9.580092e-04 563 910 54
## 227 query_1 TRUE 9.600923e-04 197 910 28
## 228 query_1 TRUE 1.146576e-03 140 910 23
## 229 query_1 TRUE 1.146576e-03 140 910 23
## 230 query_1 TRUE 1.212462e-03 276 910 34
## 231 query_1 TRUE 1.318732e-03 777 910 67
## 232 query_1 TRUE 1.360636e-03 318 910 37
## 233 query_1 TRUE 1.399842e-03 418 910 44
## 234 query_1 TRUE 1.420283e-03 31 910 11
## 235 query_1 TRUE 1.426178e-03 1351 910 100
## 236 query_1 TRUE 1.740209e-03 883 910 73
## 237 query_1 TRUE 1.817223e-03 228 910 30
## 238 query_1 TRUE 1.901885e-03 7 910 6
## 239 query_1 TRUE 1.948196e-03 379 910 41
## 240 query_1 TRUE 2.137003e-03 1254 910 94
## 241 query_1 TRUE 2.150078e-03 296 910 35
## 242 query_1 TRUE 2.250850e-03 500 910 49
## 243 query_1 TRUE 2.292001e-03 55 910 14
## 244 query_1 TRUE 2.701708e-03 124 910 21
## 245 query_1 TRUE 2.781496e-03 1154 910 88
## 246 query_1 TRUE 2.814543e-03 83 910 17
## 247 query_1 TRUE 2.893607e-03 399 910 42
## 248 query_1 TRUE 2.966770e-03 711 910 62
## 249 query_1 TRUE 2.966770e-03 711 910 62
## 250 query_1 TRUE 4.009425e-03 800 910 67
## 251 query_1 TRUE 4.043835e-03 1980 910 132
## 252 query_1 TRUE 4.131303e-03 1828 910 124
## 253 query_1 TRUE 4.628609e-03 922 910 74
## 254 query_1 TRUE 6.329273e-03 580 910 53
## 255 query_1 TRUE 6.588232e-03 913 910 73
## 256 query_1 TRUE 6.790326e-03 310 910 35
## 257 query_1 TRUE 6.812261e-03 51 910 13
## 258 query_1 TRUE 6.853110e-03 1469 910 104
## 259 query_1 TRUE 6.936904e-03 1359 910 98
## 260 query_1 TRUE 7.333668e-03 8 910 6
## 261 query_1 TRUE 8.394634e-03 29 910 10
## 262 query_1 TRUE 8.478030e-03 327 910 36
## 263 query_1 TRUE 9.205438e-03 44 910 12
## 264 query_1 TRUE 9.521462e-03 785 910 65
## 265 query_1 TRUE 9.701535e-03 111 910 19
## 266 query_1 TRUE 1.101852e-02 71 910 15
## 267 query_1 TRUE 1.171062e-02 275 910 32
## 268 query_1 TRUE 1.187445e-02 435 910 43
## 269 query_1 TRUE 1.253450e-02 825 910 67
## 270 query_1 TRUE 1.305420e-02 249 910 30
## 271 query_1 TRUE 1.462365e-02 880 910 70
## 272 query_1 TRUE 1.489665e-02 18 910 8
## 273 query_1 TRUE 1.492067e-02 4314 910 244
## 274 query_1 TRUE 1.603866e-02 149 910 22
## 275 query_1 TRUE 1.758666e-02 681 910 58
## 276 query_1 TRUE 2.477568e-02 19 910 8
## 277 query_1 TRUE 2.579657e-02 1178 910 86
## 278 query_1 TRUE 2.767867e-02 57 910 13
## 279 query_1 TRUE 2.885507e-02 560 910 50
## 280 query_1 TRUE 3.130014e-02 14 910 7
## 281 query_1 TRUE 3.130014e-02 14 910 7
## 282 query_1 TRUE 3.227865e-02 530 910 48
## 283 query_1 TRUE 3.945747e-02 319 910 34
## 284 query_1 TRUE 3.976110e-02 20 910 8
## 285 query_1 TRUE 4.181594e-02 379 910 38
## 286 query_1 TRUE 4.259375e-02 633 910 54
## 287 query_1 TRUE 4.916077e-02 998 910 75
## 288 query_1 TRUE 5.380996e-68 1149 910 203
## 289 query_1 TRUE 1.283665e-66 1344 910 218
## 290 query_1 TRUE 3.207161e-61 478 910 127
## 291 query_1 TRUE 1.974705e-57 3472 910 350
## 292 query_1 TRUE 1.061042e-56 666 910 143
## 293 query_1 TRUE 1.262341e-56 3804 910 368
## 294 query_1 TRUE 2.815699e-54 838 910 157
## 295 query_1 TRUE 3.381468e-54 102 910 62
## 296 query_1 TRUE 5.014714e-51 98 910 59
## 297 query_1 TRUE 2.512821e-37 5323 910 409
## 298 query_1 TRUE 2.884809e-25 12660 910 695
## 299 query_1 TRUE 1.077994e-24 14756 910 769
## 300 query_1 TRUE 4.761550e-10 947 910 94
## 301 query_1 TRUE 9.418197e-09 886 910 87
## 302 query_1 TRUE 7.408544e-07 292 910 41
## 303 query_1 TRUE 3.558083e-06 1661 910 126
## 304 query_1 TRUE 2.958114e-05 1554 910 117
## 305 query_1 TRUE 7.658391e-04 899 910 75
## 306 query_1 TRUE 7.333668e-03 8 910 6
## 307 query_1 TRUE 1.114734e-02 389 910 40
## 308 query_1 TRUE 1.114734e-02 389 910 40
## 309 query_1 TRUE 2.542119e-02 313 910 34
## 310 query_1 TRUE 2.737989e-02 314 910 34
## 311 query_1 TRUE 1.869022e-51 101 910 60
## 312 query_1 TRUE 2.209848e-49 156 910 70
## 313 query_1 TRUE 8.318160e-25 1163 910 139
## 314 query_1 TRUE 6.119202e-13 7203 910 426
## 315 query_1 TRUE 8.928458e-12 646 910 77
## 316 query_1 TRUE 8.928458e-12 646 910 77
## 317 query_1 TRUE 1.440857e-10 515 910 65
## 318 query_1 TRUE 1.367363e-09 19 910 13
## 319 query_1 TRUE 4.595280e-09 9204 910 498
## 320 query_1 TRUE 5.324088e-08 113 910 26
## 321 query_1 TRUE 5.337458e-07 14454 910 702
## 322 query_1 TRUE 3.957219e-04 9 910 7
## 323 query_1 TRUE 1.901885e-03 7 910 6
## 324 query_1 TRUE 2.120956e-02 9 910 6
## 325 query_1 TRUE 3.878314e-02 6 910 5
## 326 query_1 TRUE 2.379562e-09 73 910 21
## 327 query_1 TRUE 1.533598e-07 98 910 22
## 328 query_1 TRUE 3.508846e-07 102 910 22
## 329 query_1 TRUE 8.143541e-06 63 910 16
## 330 query_1 TRUE 1.119079e-04 330 910 37
## 331 query_1 TRUE 1.207102e-04 935 910 75
## 332 query_1 TRUE 2.073944e-04 426 910 43
## 333 query_1 TRUE 6.181532e-04 116 910 19
## 334 query_1 TRUE 9.342781e-04 404 910 40
## 335 query_1 TRUE 1.888432e-03 325 910 34
## 336 query_1 TRUE 4.093321e-03 7 910 5
## 337 query_1 TRUE 8.736347e-03 523 910 45
## 338 query_1 TRUE 9.283125e-03 80 910 14
## 339 query_1 TRUE 1.023961e-02 103 910 16
## 340 query_1 TRUE 1.126553e-02 206 910 24
## 341 query_1 TRUE 1.128691e-02 663 910 53
## 342 query_1 TRUE 1.136332e-02 179 910 22
## 343 query_1 TRUE 1.225641e-02 497 910 43
## 344 query_1 TRUE 1.284227e-02 581 910 48
## 345 query_1 TRUE 1.801603e-02 284 910 29
## 346 query_1 TRUE 1.824896e-02 44 910 10
## 347 query_1 TRUE 2.057702e-02 54 910 11
## 348 query_1 TRUE 2.212549e-02 75 910 13
## 349 query_1 TRUE 2.257996e-02 45 910 10
## 350 query_1 TRUE 2.293933e-02 187 910 22
## 351 query_1 TRUE 2.689239e-02 99 910 15
## 352 query_1 TRUE 2.879738e-02 1540 910 99
## 353 query_1 TRUE 2.929264e-02 634 910 50
## 354 query_1 TRUE 3.056490e-02 277 910 28
## 355 query_1 TRUE 3.101164e-02 1030 910 72
## 356 query_1 TRUE 3.263438e-02 125 910 17
## 357 query_1 TRUE 3.597157e-02 1241 910 83
## 358 query_1 TRUE 3.609563e-02 22 910 7
## 359 query_1 TRUE 3.770681e-02 193 910 22
## 360 query_1 TRUE 3.899523e-02 422 910 37
## 361 query_1 TRUE 4.775453e-02 182 910 21
## 362 query_1 TRUE 4.939313e-02 129 910 17
## 363 query_1 TRUE 4.939313e-02 129 910 17
## 364 query_1 TRUE 4.120516e-16 84 910 28
## 365 query_1 TRUE 7.832364e-10 49 910 17
## 366 query_1 TRUE 9.356325e-09 49 910 16
## 367 query_1 TRUE 3.538181e-08 53 910 16
## 368 query_1 TRUE 1.401678e-07 50 910 15
## 369 query_1 TRUE 4.534573e-07 21 910 10
## 370 query_1 TRUE 9.941072e-07 6424 910 350
## 371 query_1 TRUE 6.254301e-06 170 910 25
## 372 query_1 TRUE 8.507525e-06 75 910 16
## 373 query_1 TRUE 1.175361e-05 42 910 12
## 374 query_1 TRUE 1.355057e-05 68 910 15
## 375 query_1 TRUE 1.583606e-05 154 910 23
## 376 query_1 TRUE 2.134250e-05 219 910 28
## 377 query_1 TRUE 2.839290e-05 102 910 18
## 378 query_1 TRUE 2.861312e-05 159 910 23
## 379 query_1 TRUE 5.281831e-05 75 910 15
## 380 query_1 TRUE 5.281831e-05 75 910 15
## 381 query_1 TRUE 5.858933e-05 48 910 12
## 382 query_1 TRUE 1.056442e-04 69 910 14
## 383 query_1 TRUE 1.164287e-04 135 910 20
## 384 query_1 TRUE 1.846288e-04 53 910 12
## 385 query_1 TRUE 4.652143e-04 160 910 21
## 386 query_1 TRUE 1.076576e-03 106 910 16
## 387 query_1 TRUE 1.227049e-03 35 910 9
## 388 query_1 TRUE 1.822909e-03 202 910 23
## 389 query_1 TRUE 2.140722e-03 77 910 13
## 390 query_1 TRUE 3.140423e-03 103 910 15
## 391 query_1 TRUE 6.048828e-03 33 910 8
## 392 query_1 TRUE 2.051170e-02 121 910 15
## 393 query_1 TRUE 2.495075e-02 61 910 10
## 394 query_1 TRUE 2.632243e-02 85 910 12
## 395 query_1 TRUE 3.753069e-02 200 910 20
## 396 query_1 TRUE 2.269117e-02 28 910 7
## 397 query_1 TRUE 8.071459e-50 103 910 58
## 398 query_1 TRUE 1.307235e-49 95 910 56
## 399 query_1 TRUE 5.241522e-49 101 910 57
## 400 query_1 TRUE 1.690470e-48 181 910 72
## 401 query_1 TRUE 2.390845e-48 86 910 53
## 402 query_1 TRUE 1.452178e-47 110 910 58
## 403 query_1 TRUE 3.123739e-46 96 910 54
## 404 query_1 TRUE 9.783516e-46 102 910 55
## 405 query_1 TRUE 1.159642e-45 89 910 52
## 406 query_1 TRUE 2.666324e-45 179 910 69
## 407 query_1 TRUE 1.307052e-44 92 910 52
## 408 query_1 TRUE 6.415408e-44 108 910 55
## 409 query_1 TRUE 1.154961e-42 98 910 52
## 410 query_1 TRUE 5.646062e-42 110 910 54
## 411 query_1 TRUE 2.362007e-40 111 910 53
## 412 query_1 TRUE 2.493838e-39 115 910 53
## 413 query_1 TRUE 9.876826e-38 157 910 59
## 414 query_1 TRUE 3.310412e-37 852 910 132
## 415 query_1 TRUE 1.719433e-35 138 910 54
## 416 query_1 TRUE 2.176755e-35 177 910 60
## 417 query_1 TRUE 6.354049e-33 1430 910 169
## 418 query_1 TRUE 1.848646e-31 526 910 95
## 419 query_1 TRUE 3.314956e-30 155 910 52
## 420 query_1 TRUE 9.453461e-29 194 910 56
## 421 query_1 TRUE 8.041589e-26 701 910 102
## 422 query_1 TRUE 4.395615e-15 589 910 75
## 423 query_1 TRUE 1.885947e-14 7123 910 420
## 424 query_1 TRUE 1.014714e-09 429 910 53
## 425 query_1 TRUE 9.112679e-08 7 910 7
## 426 query_1 TRUE 5.897775e-06 183 910 27
## 427 query_1 TRUE 9.774368e-06 10 910 7
## 428 query_1 TRUE 9.774368e-06 10 910 7
## 429 query_1 TRUE 3.382430e-05 405 910 42
## 430 query_1 TRUE 5.986280e-05 230 910 29
## 431 query_1 TRUE 7.197754e-05 61 910 14
## 432 query_1 TRUE 1.142274e-04 1814 910 121
## 433 query_1 TRUE 2.103050e-04 40 910 11
## 434 query_1 TRUE 5.711369e-04 388 910 38
## 435 query_1 TRUE 1.223380e-03 4 910 4
## 436 query_1 TRUE 1.870389e-03 49 910 11
## 437 query_1 TRUE 5.945019e-03 110 910 16
## 438 query_1 TRUE 2.901448e-02 3 910 3
## 439 query_1 TRUE 2.901448e-02 3 910 3
## 440 query_1 TRUE 2.954941e-02 26 910 7
## 441 query_1 TRUE 3.237900e-02 126 910 16
## 442 query_1 TRUE 4.734864e-02 372 910 32
## 443 query_1 TRUE 7.681253e-10 3295 910 226
## 444 query_1 TRUE 1.263980e-08 9484 910 508
## 445 query_1 TRUE 2.646950e-07 6765 910 382
## 446 query_1 TRUE 4.520655e-07 5211 910 309
## 447 query_1 TRUE 7.011235e-07 4997 910 298
## 448 query_1 TRUE 1.661656e-06 10553 910 543
## 449 query_1 TRUE 1.822376e-06 14204 910 690
## 450 query_1 TRUE 1.822376e-06 14204 910 690
## 451 query_1 TRUE 3.012456e-06 15518 910 739
## 452 query_1 TRUE 3.059451e-06 15492 910 738
## 453 query_1 TRUE 3.200389e-06 15521 910 739
## 454 query_1 TRUE 3.268510e-06 3614 910 228
## 455 query_1 TRUE 3.952190e-06 12349 910 615
## 456 query_1 TRUE 4.262996e-06 13658 910 667
## 457 query_1 TRUE 5.035020e-06 10421 910 535
## 458 query_1 TRUE 5.890273e-06 15498 910 737
## 459 query_1 TRUE 7.468584e-06 4971 910 292
## 460 query_1 TRUE 9.004741e-06 13041 910 641
## 461 query_1 TRUE 1.551913e-05 9655 910 500
## 462 query_1 TRUE 1.685600e-05 15392 910 731
## 463 query_1 TRUE 1.781745e-05 9686 910 501
## 464 query_1 TRUE 2.616055e-05 11279 910 567
## 465 query_1 TRUE 2.616055e-05 11279 910 567
## 466 query_1 TRUE 6.672789e-05 10113 910 516
## 467 query_1 TRUE 7.677311e-05 13638 910 660
## 468 query_1 TRUE 1.588008e-04 5584 910 314
## 469 query_1 TRUE 1.777576e-04 7943 910 420
## 470 query_1 TRUE 1.909140e-04 9305 910 479
## 471 query_1 TRUE 1.917258e-04 7292 910 391
## 472 query_1 TRUE 2.027205e-04 10724 910 539
## 473 query_1 TRUE 2.344776e-04 9879 910 503
## 474 query_1 TRUE 2.422514e-04 6282 910 345
## 475 query_1 TRUE 3.156362e-04 2048 910 140
## 476 query_1 TRUE 3.643972e-04 14057 910 673
## 477 query_1 TRUE 3.817160e-04 8100 910 425
## 478 query_1 TRUE 5.081569e-04 11840 910 583
## 479 query_1 TRUE 6.254859e-04 15377 910 723
## 480 query_1 TRUE 6.450919e-04 12074 910 592
## 481 query_1 TRUE 6.996806e-04 7274 910 387
## 482 query_1 TRUE 7.285932e-04 4104 910 241
## 483 query_1 TRUE 7.336249e-04 9900 910 501
## 484 query_1 TRUE 7.336249e-04 9900 910 501
## 485 query_1 TRUE 8.375653e-04 4871 910 277
## 486 query_1 TRUE 9.230020e-04 10935 910 544
## 487 query_1 TRUE 9.621147e-04 5916 910 325
## 488 query_1 TRUE 1.548641e-03 9011 910 461
## 489 query_1 TRUE 1.681452e-03 4586 910 262
## 490 query_1 TRUE 1.823669e-03 6858 910 366
## 491 query_1 TRUE 1.942358e-03 5171 910 289
## 492 query_1 TRUE 1.942358e-03 5171 910 289
## 493 query_1 TRUE 1.942358e-03 5171 910 289
## 494 query_1 TRUE 1.975297e-03 6573 910 353
## 495 query_1 TRUE 2.048093e-03 2818 910 176
## 496 query_1 TRUE 2.301288e-03 8023 910 417
## 497 query_1 TRUE 3.927196e-03 6103 910 330
## 498 query_1 TRUE 4.684694e-03 5674 910 310
## 499 query_1 TRUE 6.306465e-03 1338 910 97
## 500 query_1 TRUE 6.319437e-03 11635 910 568
## 501 query_1 TRUE 7.522892e-03 2079 910 136
## 502 query_1 TRUE 9.687174e-03 14106 910 667
## 503 query_1 TRUE 1.067006e-02 4552 910 256
## 504 query_1 TRUE 1.070321e-02 13039 910 624
## 505 query_1 TRUE 1.070321e-02 13039 910 624
## 506 query_1 TRUE 1.070321e-02 13039 910 624
## 507 query_1 TRUE 1.094972e-02 2746 910 169
## 508 query_1 TRUE 1.099368e-02 7099 910 372
## 509 query_1 TRUE 1.163534e-02 7080 910 371
## 510 query_1 TRUE 1.386145e-02 11470 910 559
## 511 query_1 TRUE 1.527436e-02 10591 910 522
## 512 query_1 TRUE 1.527436e-02 10591 910 522
## 513 query_1 TRUE 1.527436e-02 10591 910 522
## 514 query_1 TRUE 1.713783e-02 3090 910 185
## 515 query_1 TRUE 1.877035e-02 8292 910 423
## 516 query_1 TRUE 1.877035e-02 8292 910 423
## 517 query_1 TRUE 1.933349e-02 4031 910 230
## 518 query_1 TRUE 1.987933e-02 870 910 69
## 519 query_1 TRUE 2.188162e-02 12228 910 589
## 520 query_1 TRUE 2.631632e-02 4815 910 266
## 521 query_1 TRUE 3.305068e-02 7078 910 368
## 522 query_1 TRUE 3.707074e-02 8891 910 447
## 523 query_1 TRUE 3.721373e-02 8683 910 438
## 524 query_1 TRUE 3.786919e-02 7403 910 382
## 525 query_1 TRUE 4.283009e-02 1968 910 127
## 526 query_1 TRUE 4.501087e-02 15044 910 700
## 527 query_1 TRUE 4.734723e-02 3034 910 180
## 528 query_1 TRUE 4.783054e-02 2973 910 177
## 529 query_1 TRUE 4.836775e-02 6430 910 338
## 530 query_1 TRUE 1.987135e-08 3661 910 227
## 531 query_1 TRUE 1.811430e-05 174 910 24
## 532 query_1 TRUE 2.400904e-05 106 910 18
## 533 query_1 TRUE 3.767607e-05 41 910 11
## 534 query_1 TRUE 2.641333e-04 162 910 21
## 535 query_1 TRUE 5.712605e-04 53 910 11
## 536 query_1 TRUE 8.300878e-04 55 910 11
## 537 query_1 TRUE 7.301666e-03 173 910 19
## 538 query_1 TRUE 2.852221e-02 10 910 4
## 539 query_1 TRUE 4.584493e-02 98 910 12
## precision recall term_id source
## 1 0.003296703 1.00000000 CORUM:2900 CORUM
## 2 0.003296703 0.75000000 CORUM:2742 CORUM
## 3 0.002197802 1.00000000 CORUM:2868 CORUM
## 4 0.280219780 0.19721578 GO:0006955 GO:BP
## 5 0.362637363 0.15034169 GO:0002376 GO:BP
## 6 0.558241758 0.08238729 GO:0050896 GO:BP
## 7 0.084615385 0.55000000 GO:0050853 GO:BP
## 8 0.127472527 0.28501229 GO:0002443 GO:BP
## 9 0.212087912 0.15963606 GO:0006952 GO:BP
## 10 0.142857143 0.23550725 GO:0045087 GO:BP
## 11 0.104395604 0.34545455 GO:0002429 GO:BP
## 12 0.105494505 0.34042553 GO:0002768 GO:BP
## 13 0.104395604 0.34420290 GO:0002757 GO:BP
## 14 0.167032967 0.19387755 GO:0098542 GO:BP
## 15 0.124175824 0.26588235 GO:0002764 GO:BP
## 16 0.178021978 0.17685590 GO:0045321 GO:BP
## 17 0.196703297 0.16111611 GO:0051707 GO:BP
## 18 0.196703297 0.16082659 GO:0043207 GO:BP
## 19 0.143956044 0.21760797 GO:0002252 GO:BP
## 20 0.185714286 0.16799205 GO:0001775 GO:BP
## 21 0.197802198 0.15789474 GO:0009607 GO:BP
## 22 0.205494505 0.15265306 GO:0044419 GO:BP
## 23 0.274725275 0.12030799 GO:0009605 GO:BP
## 24 0.107692308 0.28908555 GO:0002253 GO:BP
## 25 0.167032967 0.17736289 GO:0002684 GO:BP
## 26 0.104395604 0.29320988 GO:0002449 GO:BP
## 27 0.130769231 0.22537879 GO:0050778 GO:BP
## 28 0.157142857 0.18499353 GO:0050776 GO:BP
## 29 0.091208791 0.34297521 GO:0050851 GO:BP
## 30 0.249450549 0.12283550 GO:0048584 GO:BP
## 31 0.156043956 0.18205128 GO:0046649 GO:BP
## 32 0.072527473 0.45517241 GO:0006911 GO:BP
## 33 0.204395604 0.14274751 GO:0002682 GO:BP
## 34 0.073626374 0.43790850 GO:0099024 GO:BP
## 35 0.065934066 0.51282051 GO:0006910 GO:BP
## 36 0.062637363 0.54807692 GO:0006958 GO:BP
## 37 0.093406593 0.30797101 GO:0042742 GO:BP
## 38 0.136263736 0.20064725 GO:0002694 GO:BP
## 39 0.382417582 0.09015544 GO:0007165 GO:BP
## 40 0.073626374 0.42138365 GO:0010324 GO:BP
## 41 0.137362637 0.19623234 GO:0009617 GO:BP
## 42 0.139560440 0.19213313 GO:0050865 GO:BP
## 43 0.063736264 0.49572650 GO:0002455 GO:BP
## 44 0.098901099 0.27190332 GO:0042113 GO:BP
## 45 0.081318681 0.34259259 GO:0050864 GO:BP
## 46 0.103296703 0.25268817 GO:0002250 GO:BP
## 47 0.063736264 0.46774194 GO:0006956 GO:BP
## 48 0.398901099 0.08511137 GO:0023052 GO:BP
## 49 0.121978022 0.20825516 GO:0051249 GO:BP
## 50 0.090109890 0.29078014 GO:0006909 GO:BP
## 51 0.400000000 0.08437645 GO:0007154 GO:BP
## 52 0.254945055 0.11005693 GO:0007166 GO:BP
## 53 0.107692308 0.22897196 GO:0002696 GO:BP
## 54 0.108791209 0.22347630 GO:0050867 GO:BP
## 55 0.325274725 0.09352291 GO:0048583 GO:BP
## 56 0.095604396 0.25513196 GO:0002460 GO:BP
## 57 0.073626374 0.34010152 GO:0019724 GO:BP
## 58 0.069230769 0.36627907 GO:0050871 GO:BP
## 59 0.072527473 0.34196891 GO:0016064 GO:BP
## 60 0.098901099 0.23560209 GO:0051251 GO:BP
## 61 0.075824176 0.31221719 GO:0006959 GO:BP
## 62 0.069230769 0.30882353 GO:0008037 GO:BP
## 63 0.420879121 0.07511277 GO:0048518 GO:BP
## 64 0.420879121 0.07484854 GO:0051716 GO:BP
## 65 0.292307692 0.09004739 GO:0006950 GO:BP
## 66 0.100000000 0.18346774 GO:0006897 GO:BP
## 67 0.381318681 0.07548401 GO:0048522 GO:BP
## 68 0.598901099 0.06160280 GO:0065007 GO:BP
## 69 0.570329670 0.06172693 GO:0050789 GO:BP
## 70 0.846153846 0.05193229 GO:0008150 GO:BP
## 71 0.528571429 0.06045752 GO:0050794 GO:BP
## 72 0.143956044 0.10421639 GO:0016192 GO:BP
## 73 0.138461538 0.10153102 GO:0016477 GO:BP
## 74 0.097802198 0.12258953 GO:0061024 GO:BP
## 75 0.142857143 0.09502924 GO:0048870 GO:BP
## 76 0.267032967 0.07151265 GO:0048731 GO:BP
## 77 0.098901099 0.11306533 GO:0032101 GO:BP
## 78 0.202197802 0.07893608 GO:0051239 GO:BP
## 79 0.096703297 0.11267606 GO:0022603 GO:BP
## 80 0.076923077 0.12962963 GO:0006954 GO:BP
## 81 0.046153846 0.19444444 GO:0002703 GO:BP
## 82 0.362637363 0.06308545 GO:0032501 GO:BP
## 83 0.061538462 0.14432990 GO:0032103 GO:BP
## 84 0.115384615 0.09713228 GO:0040011 GO:BP
## 85 0.131868132 0.09090909 GO:0051240 GO:BP
## 86 0.108791209 0.09900000 GO:0007155 GO:BP
## 87 0.246153846 0.07002188 GO:0048869 GO:BP
## 88 0.056043956 0.15000000 GO:0002697 GO:BP
## 89 0.250549451 0.06925881 GO:0006810 GO:BP
## 90 0.242857143 0.06956248 GO:0030154 GO:BP
## 91 0.257142857 0.06818182 GO:0051234 GO:BP
## 92 0.047252747 0.16666667 GO:0031349 GO:BP
## 93 0.097802198 0.10183066 GO:0048534 GO:BP
## 94 0.665934066 0.05180816 GO:0009987 GO:BP
## 95 0.052747253 0.15141956 GO:0050900 GO:BP
## 96 0.045054945 0.17226891 GO:0002699 GO:BP
## 97 0.216483516 0.07179300 GO:0048513 GO:BP
## 98 0.094505495 0.10274791 GO:0030097 GO:BP
## 99 0.308791209 0.06379115 GO:0048856 GO:BP
## 100 0.176923077 0.07695985 GO:0050793 GO:BP
## 101 0.035164835 0.20779221 GO:0001906 GO:BP
## 102 0.100000000 0.09795479 GO:0002520 GO:BP
## 103 0.040659341 0.17961165 GO:0002274 GO:BP
## 104 0.038461538 0.18617021 GO:0030595 GO:BP
## 105 0.069230769 0.11842105 GO:0031347 GO:BP
## 106 0.179120879 0.07501150 GO:0009653 GO:BP
## 107 0.271428571 0.06524036 GO:0007275 GO:BP
## 108 0.225274725 0.06904682 GO:0042221 GO:BP
## 109 0.119780220 0.08790323 GO:0009967 GO:BP
## 110 0.043956044 0.16064257 GO:0060326 GO:BP
## 111 0.038461538 0.17948718 GO:0097529 GO:BP
## 112 0.131868132 0.08362369 GO:0010647 GO:BP
## 113 0.062637363 0.12337662 GO:0006935 GO:BP
## 114 0.062637363 0.12311015 GO:0042330 GO:BP
## 115 0.069230769 0.11559633 GO:0002521 GO:BP
## 116 0.131868132 0.08333333 GO:0023056 GO:BP
## 117 0.161538462 0.07684266 GO:0035556 GO:BP
## 118 0.184615385 0.07313888 GO:0009966 GO:BP
## 119 0.076923077 0.10819165 GO:0001816 GO:BP
## 120 0.183516484 0.07289393 GO:0010033 GO:BP
## 121 0.012087912 0.73333333 GO:0002220 GO:BP
## 122 0.328571429 0.06092095 GO:0016043 GO:BP
## 123 0.010989011 0.83333333 GO:0002223 GO:BP
## 124 0.010989011 0.83333333 GO:1990858 GO:BP
## 125 0.010989011 0.83333333 GO:1990840 GO:BP
## 126 0.318681319 0.06128487 GO:0032502 GO:BP
## 127 0.021978022 0.30769231 GO:0043299 GO:BP
## 128 0.026373626 0.24742268 GO:0031341 GO:BP
## 129 0.027472527 0.23148148 GO:0001909 GO:BP
## 130 0.012087912 0.68750000 GO:0002758 GO:BP
## 131 0.041758242 0.15702479 GO:0045765 GO:BP
## 132 0.074725275 0.10608424 GO:0001817 GO:BP
## 133 0.041758242 0.15510204 GO:1901342 GO:BP
## 134 0.276923077 0.06298425 GO:0051179 GO:BP
## 135 0.069230769 0.10956522 GO:0010942 GO:BP
## 136 0.183516484 0.07118500 GO:0070887 GO:BP
## 137 0.054945055 0.12531328 GO:0001525 GO:BP
## 138 0.018681319 0.34693878 GO:0043300 GO:BP
## 139 0.201098901 0.06892655 GO:0023051 GO:BP
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## 141 0.075824176 0.10283159 GO:0098609 GO:BP
## 142 0.074725275 0.10334347 GO:0030155 GO:BP
## 143 0.200000000 0.06875708 GO:0010646 GO:BP
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## 146 0.329670330 0.05935892 GO:0071840 GO:BP
## 147 0.018681319 0.32692308 GO:0002715 GO:BP
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## 150 0.021978022 0.25974026 GO:0001910 GO:BP
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## 159 0.019780220 0.27272727 GO:0031343 GO:BP
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## 290 0.139560440 0.26569038 GO:0009897 GO:CC
## 291 0.384615385 0.10080645 GO:0005886 GO:CC
## 292 0.157142857 0.21471471 GO:0098552 GO:CC
## 293 0.404395604 0.09674027 GO:0071944 GO:CC
## 294 0.172527473 0.18735084 GO:0009986 GO:CC
## 295 0.068131868 0.60784314 GO:0019814 GO:CC
## 296 0.064835165 0.60204082 GO:0042571 GO:CC
## 297 0.449450549 0.07683637 GO:0016020 GO:CC
## 298 0.763736264 0.05489731 GO:0110165 GO:CC
## 299 0.845054945 0.05211439 GO:0005575 GO:CC
## 300 0.103296703 0.09926082 GO:0031226 GO:CC
## 301 0.095604396 0.09819413 GO:0005887 GO:CC
## 302 0.045054945 0.14041096 GO:0043235 GO:CC
## 303 0.138461538 0.07585792 GO:0031224 GO:CC
## 304 0.128571429 0.07528958 GO:0016021 GO:CC
## 305 0.082417582 0.08342603 GO:0098590 GO:CC
## 306 0.006593407 0.75000000 GO:0042613 GO:CC
## 307 0.043956044 0.10282776 GO:0005764 GO:CC
## 308 0.043956044 0.10282776 GO:0000323 GO:CC
## 309 0.037362637 0.10862620 GO:0045121 GO:CC
## 310 0.037362637 0.10828025 GO:0098857 GO:CC
## 311 0.065934066 0.59405941 GO:0034987 GO:MF
## 312 0.076923077 0.44871795 GO:0003823 GO:MF
## 313 0.152747253 0.11951849 GO:0005102 GO:MF
## 314 0.468131868 0.05914202 GO:0005515 GO:MF
## 315 0.084615385 0.11919505 GO:0060089 GO:MF
## 316 0.084615385 0.11919505 GO:0038023 GO:MF
## 317 0.071428571 0.12621359 GO:0004888 GO:MF
## 318 0.014285714 0.68421053 GO:0023023 GO:MF
## 319 0.547252747 0.05410691 GO:0005488 GO:MF
## 320 0.028571429 0.23008850 GO:0140375 GO:MF
## 321 0.771428571 0.04856787 GO:0003674 GO:MF
## 322 0.007692308 0.77777778 GO:0032394 GO:MF
## 323 0.006593407 0.85714286 GO:0023024 GO:MF
## 324 0.006593407 0.66666667 GO:0023026 GO:MF
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## 328 0.024175824 0.21568627 HP:0032158 HP
## 329 0.017582418 0.25396825 HP:0002633 HP
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## 333 0.020879121 0.16379310 HP:0000988 HP
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## 336 0.005494505 0.71428571 HP:0004444 HP
## 337 0.049450549 0.08604207 HP:0001743 HP
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## 340 0.026373626 0.11650485 HP:0002733 HP
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## 342 0.024175824 0.12290503 HP:0002960 HP
## 343 0.047252747 0.08651911 HP:0025408 HP
## 344 0.052747253 0.08261618 HP:0011032 HP
## 345 0.031868132 0.10211268 HP:0002027 HP
## 346 0.010989011 0.22727273 HP:0100658 HP
## 347 0.012087912 0.20370370 HP:0002720 HP
## 348 0.014285714 0.17333333 HP:0410243 HP
## 349 0.010989011 0.22222222 HP:0002850 HP
## 350 0.024175824 0.11764706 HP:0001369 HP
## 351 0.016483516 0.15151515 HP:0000509 HP
## 352 0.108791209 0.06428571 HP:0000006 HP
## 353 0.054945055 0.07886435 HP:0100763 HP
## 354 0.030769231 0.10108303 HP:0002315 HP
## 355 0.079120879 0.06990291 HP:0002088 HP
## 356 0.018681319 0.13600000 HP:0002110 HP
## 357 0.091208791 0.06688155 HP:0001871 HP
## 358 0.007692308 0.31818182 HP:0004432 HP
## 359 0.024175824 0.11398964 HP:0002716 HP
## 360 0.040659341 0.08767773 HP:0011122 HP
## 361 0.023076923 0.11538462 HP:0100533 HP
## 362 0.018681319 0.13178295 HP:0011895 HP
## 363 0.018681319 0.13178295 HP:0001878 HP
## 364 0.030769231 0.33333333 KEGG:04640 KEGG
## 365 0.018681319 0.34693878 KEGG:05332 KEGG
## 366 0.017582418 0.32653061 KEGG:05330 KEGG
## 367 0.017582418 0.30188679 KEGG:04940 KEGG
## 368 0.016483516 0.30000000 KEGG:05320 KEGG
## 369 0.010989011 0.47619048 KEGG:05310 KEGG
## 370 0.384615385 0.05448319 KEGG:00000 KEGG
## 371 0.027472527 0.14705882 KEGG:04062 KEGG
## 372 0.017582418 0.21333333 KEGG:04612 KEGG
## 373 0.013186813 0.28571429 KEGG:04672 KEGG
## 374 0.016483516 0.22058824 KEGG:05140 KEGG
## 375 0.025274725 0.14935065 KEGG:04145 KEGG
## 376 0.030769231 0.12785388 KEGG:04060 KEGG
## 377 0.019780220 0.17647059 KEGG:04650 KEGG
## 378 0.025274725 0.14465409 KEGG:05152 KEGG
## 379 0.016483516 0.20000000 KEGG:04662 KEGG
## 380 0.016483516 0.20000000 KEGG:04061 KEGG
## 381 0.013186813 0.25000000 KEGG:05150 KEGG
## 382 0.015384615 0.20289855 KEGG:05416 KEGG
## 383 0.021978022 0.14814815 KEGG:04514 KEGG
## 384 0.013186813 0.22641509 KEGG:05144 KEGG
## 385 0.023076923 0.13125000 KEGG:05202 KEGG
## 386 0.017582418 0.15094340 KEGG:05145 KEGG
## 387 0.009890110 0.25714286 KEGG:05340 KEGG
## 388 0.025274725 0.11386139 KEGG:05169 KEGG
## 389 0.014285714 0.16883117 KEGG:05323 KEGG
## 390 0.016483516 0.14563107 KEGG:04625 KEGG
## 391 0.008791209 0.24242424 KEGG:05143 KEGG
## 392 0.016483516 0.12396694 KEGG:04380 KEGG
## 393 0.010989011 0.16393443 KEGG:05321 KEGG
## 394 0.013186813 0.14117647 KEGG:04658 KEGG
## 395 0.021978022 0.10000000 KEGG:04014 KEGG
## 396 0.007692308 0.25000000 MIRNA:mmu-miR-27b-3p MIRNA
## 397 0.063736264 0.56310680 REAC:R-MMU-983695 REAC
## 398 0.061538462 0.58947368 REAC:R-MMU-2029481 REAC
## 399 0.062637363 0.56435644 REAC:R-MMU-2168880 REAC
## 400 0.079120879 0.39779006 REAC:R-MMU-198933 REAC
## 401 0.058241758 0.61627907 REAC:R-MMU-5690714 REAC
## 402 0.063736264 0.52727273 REAC:R-MMU-2173782 REAC
## 403 0.059340659 0.56250000 REAC:R-MMU-2730905 REAC
## 404 0.060439560 0.53921569 REAC:R-MMU-2029485 REAC
## 405 0.057142857 0.58426966 REAC:R-MMU-173623 REAC
## 406 0.075824176 0.38547486 REAC:R-MMU-202733 REAC
## 407 0.057142857 0.56521739 REAC:R-MMU-166786 REAC
## 408 0.060439560 0.50925926 REAC:R-MMU-2871809 REAC
## 409 0.057142857 0.53061224 REAC:R-MMU-166663 REAC
## 410 0.059340659 0.49090909 REAC:R-MMU-2871796 REAC
## 411 0.058241758 0.47747748 REAC:R-MMU-977606 REAC
## 412 0.058241758 0.46086957 REAC:R-MMU-166658 REAC
## 413 0.064835165 0.37579618 REAC:R-MMU-2029480 REAC
## 414 0.145054945 0.15492958 REAC:R-MMU-168249 REAC
## 415 0.059340659 0.39130435 REAC:R-MMU-2029482 REAC
## 416 0.065934066 0.33898305 REAC:R-MMU-983705 REAC
## 417 0.185714286 0.11818182 REAC:R-MMU-168256 REAC
## 418 0.104395604 0.18060837 REAC:R-MMU-109582 REAC
## 419 0.057142857 0.33548387 REAC:R-MMU-2871837 REAC
## 420 0.061538462 0.28865979 REAC:R-MMU-2454202 REAC
## 421 0.112087912 0.14550642 REAC:R-MMU-1280218 REAC
## 422 0.082417582 0.12733447 REAC:R-MMU-5653656 REAC
## 423 0.461538462 0.05896392 REAC:0000000 REAC
## 424 0.058241758 0.12354312 REAC:R-MMU-6798695 REAC
## 425 0.007692308 1.00000000 REAC:R-MMU-1247673 REAC
## 426 0.029670330 0.14754098 REAC:R-MMU-373076 REAC
## 427 0.007692308 0.70000000 REAC:R-MMU-1237044 REAC
## 428 0.007692308 0.70000000 REAC:R-MMU-1480926 REAC
## 429 0.046153846 0.10370370 REAC:R-MMU-372790 REAC
## 430 0.031868132 0.12608696 REAC:R-MMU-500792 REAC
## 431 0.015384615 0.22950820 REAC:R-MMU-2172127 REAC
## 432 0.132967033 0.06670342 REAC:R-MMU-162582 REAC
## 433 0.012087912 0.27500000 REAC:R-MMU-380108 REAC
## 434 0.041758242 0.09793814 REAC:R-MMU-388396 REAC
## 435 0.004395604 1.00000000 REAC:R-MMU-6799990 REAC
## 436 0.012087912 0.22448980 REAC:R-MMU-2424491 REAC
## 437 0.017582418 0.14545455 REAC:R-MMU-375276 REAC
## 438 0.003296703 1.00000000 REAC:R-MMU-5660526 REAC
## 439 0.003296703 1.00000000 REAC:R-MMU-5661231 REAC
## 440 0.007692308 0.26923077 REAC:R-MMU-6803157 REAC
## 441 0.017582418 0.12698413 REAC:R-MMU-8980692 REAC
## 442 0.035164835 0.08602151 REAC:R-MMU-9012999 REAC
## 443 0.248351648 0.06858877 TF:M01172 TF
## 444 0.558241758 0.05356390 TF:M00646 TF
## 445 0.419780220 0.05646711 TF:M00749 TF
## 446 0.339560440 0.05929764 TF:M01808_1 TF
## 447 0.327472527 0.05963578 TF:M10270 TF
## 448 0.596703297 0.05145456 TF:M01808 TF
## 449 0.758241758 0.04857787 TF:M02031 TF
## 450 0.758241758 0.04857787 TF:M01266 TF
## 451 0.812087912 0.04762212 TF:M03851 TF
## 452 0.810989011 0.04763749 TF:M03851_1 TF
## 453 0.812087912 0.04761291 TF:M00000 TF
## 454 0.250549451 0.06308799 TF:M00658 TF
## 455 0.675824176 0.04980160 TF:M04624 TF
## 456 0.732967033 0.04883585 TF:M03848 TF
## 457 0.587912088 0.05133864 TF:M07107 TF
## 458 0.809890110 0.04755452 TF:M01160 TF
## 459 0.320879121 0.05874070 TF:M07107_1 TF
## 460 0.704395604 0.04915267 TF:M03803 TF
## 461 0.549450549 0.05178664 TF:M03541 TF
## 462 0.803296703 0.04749220 TF:M01160_1 TF
## 463 0.550549451 0.05172414 TF:M00704 TF
## 464 0.623076923 0.05027041 TF:M02031_1 TF
## 465 0.623076923 0.05027041 TF:M01266_1 TF
## 466 0.567032967 0.05102344 TF:M04636 TF
## 467 0.725274725 0.04839419 TF:M02027 TF
## 468 0.345054945 0.05623209 TF:M00221 TF
## 469 0.461538462 0.05287675 TF:M01733 TF
## 470 0.526373626 0.05147770 TF:M08793 TF
## 471 0.429670330 0.05362041 TF:M01835_1 TF
## 472 0.592307692 0.05026110 TF:M10285 TF
## 473 0.552747253 0.05091608 TF:M03848_1 TF
## 474 0.379120879 0.05491882 TF:M10218 TF
## 475 0.153846154 0.06835938 TF:M09710 TF
## 476 0.739560440 0.04787650 TF:M02941 TF
## 477 0.467032967 0.05246914 TF:M00655 TF
## 478 0.640659341 0.04923986 TF:M01835 TF
## 479 0.794505495 0.04701827 TF:M01822 TF
## 480 0.650549451 0.04903098 TF:M02895 TF
## 481 0.425274725 0.05320319 TF:M10281 TF
## 482 0.264835165 0.05872320 TF:M00646_1 TF
## 483 0.550549451 0.05060606 TF:M02101_1 TF
## 484 0.550549451 0.05060606 TF:M02101 TF
## 485 0.304395604 0.05686717 TF:M10368 TF
## 486 0.597802198 0.04974851 TF:M02941_1 TF
## 487 0.357142857 0.05493577 TF:M10285_1 TF
## 488 0.506593407 0.05115969 TF:M01020 TF
## 489 0.287912088 0.05713040 TF:M03804 TF
## 490 0.402197802 0.05336833 TF:M03577 TF
## 491 0.317582418 0.05588861 TF:M02084_1 TF
## 492 0.317582418 0.05588861 TF:M00271_1 TF
## 493 0.317582418 0.05588861 TF:M00751_1 TF
## 494 0.387912088 0.05370455 TF:M10395 TF
## 495 0.193406593 0.06245564 TF:M01733_1 TF
## 496 0.458241758 0.05197557 TF:M02006 TF
## 497 0.362637363 0.05407177 TF:M07429 TF
## 498 0.340659341 0.05463518 TF:M00339 TF
## 499 0.106593407 0.07249626 TF:M07224 TF
## 500 0.624175824 0.04881822 TF:M03819 TF
## 501 0.149450549 0.06541607 TF:M00192_1 TF
## 502 0.732967033 0.04728484 TF:M00378 TF
## 503 0.281318681 0.05623902 TF:M10273 TF
## 504 0.685714286 0.04785643 TF:M01281 TF
## 505 0.685714286 0.04785643 TF:M01886 TF
## 506 0.685714286 0.04785643 TF:M03555 TF
## 507 0.185714286 0.06154406 TF:M07461_1 TF
## 508 0.408791209 0.05240175 TF:M03841 TF
## 509 0.407692308 0.05240113 TF:M00072 TF
## 510 0.614285714 0.04873583 TF:M00378_1 TF
## 511 0.573626374 0.04928713 TF:M02084 TF
## 512 0.573626374 0.04928713 TF:M00271 TF
## 513 0.573626374 0.04928713 TF:M00751 TF
## 514 0.203296703 0.05987055 TF:M10353 TF
## 515 0.464835165 0.05101302 TF:M01207 TF
## 516 0.464835165 0.05101302 TF:M07252 TF
## 517 0.252747253 0.05705780 TF:M00701 TF
## 518 0.075824176 0.07931034 TF:M00701_1 TF
## 519 0.647252747 0.04816814 TF:M02116 TF
## 520 0.292307692 0.05524403 TF:M00084 TF
## 521 0.404395604 0.05199209 TF:M00192 TF
## 522 0.491208791 0.05027556 TF:M03580_1 TF
## 523 0.481318681 0.05044340 TF:M08888 TF
## 524 0.419780220 0.05160070 TF:M00733 TF
## 525 0.139560440 0.06453252 TF:M00971 TF
## 526 0.769230769 0.04653018 TF:M01822_1 TF
## 527 0.197802198 0.05932762 TF:M08888_1 TF
## 528 0.194505495 0.05953582 TF:M02852 TF
## 529 0.371428571 0.05256610 TF:M00033 TF
## 530 0.249450549 0.06200492 WP:000000 WP
## 531 0.026373626 0.13793103 WP:WP1396 WP
## 532 0.019780220 0.16981132 WP:WP189 WP
## 533 0.012087912 0.26829268 WP:WP3626 WP
## 534 0.023076923 0.12962963 WP:WP2292 WP
## 535 0.012087912 0.20754717 WP:WP3632 WP
## 536 0.012087912 0.20000000 WP:WP3625 WP
## 537 0.020879121 0.10982659 WP:WP85 WP
## 538 0.004395604 0.40000000 WP:WP2271 WP
## 539 0.013186813 0.12244898 WP:WP373 WP
## term_name
## 1 PLC-gamma-2-Lab-Blnk complex, BCR stimulated
## 2 Gata2-Tal1-Tcf3-Lmo2 complex
## 3 TEAD3-YAP DNA-protein complex
## 4 immune response
## 5 immune system process
## 6 response to stimulus
## 7 B cell receptor signaling pathway
## 8 leukocyte mediated immunity
## 9 defense response
## 10 innate immune response
## 11 immune response-activating cell surface receptor signaling pathway
## 12 immune response-regulating cell surface receptor signaling pathway
## 13 immune response-activating signal transduction
## 14 defense response to other organism
## 15 immune response-regulating signaling pathway
## 16 leukocyte activation
## 17 response to other organism
## 18 response to external biotic stimulus
## 19 immune effector process
## 20 cell activation
## 21 response to biotic stimulus
## 22 biological process involved in interspecies interaction between organisms
## 23 response to external stimulus
## 24 activation of immune response
## 25 positive regulation of immune system process
## 26 lymphocyte mediated immunity
## 27 positive regulation of immune response
## 28 regulation of immune response
## 29 antigen receptor-mediated signaling pathway
## 30 positive regulation of response to stimulus
## 31 lymphocyte activation
## 32 phagocytosis, engulfment
## 33 regulation of immune system process
## 34 plasma membrane invagination
## 35 phagocytosis, recognition
## 36 complement activation, classical pathway
## 37 defense response to bacterium
## 38 regulation of leukocyte activation
## 39 signal transduction
## 40 membrane invagination
## 41 response to bacterium
## 42 regulation of cell activation
## 43 humoral immune response mediated by circulating immunoglobulin
## 44 B cell activation
## 45 regulation of B cell activation
## 46 adaptive immune response
## 47 complement activation
## 48 signaling
## 49 regulation of lymphocyte activation
## 50 phagocytosis
## 51 cell communication
## 52 cell surface receptor signaling pathway
## 53 positive regulation of leukocyte activation
## 54 positive regulation of cell activation
## 55 regulation of response to stimulus
## 56 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
## 57 B cell mediated immunity
## 58 positive regulation of B cell activation
## 59 immunoglobulin mediated immune response
## 60 positive regulation of lymphocyte activation
## 61 humoral immune response
## 62 cell recognition
## 63 positive regulation of biological process
## 64 cellular response to stimulus
## 65 response to stress
## 66 endocytosis
## 67 positive regulation of cellular process
## 68 biological regulation
## 69 regulation of biological process
## 70 biological_process
## 71 regulation of cellular process
## 72 vesicle-mediated transport
## 73 cell migration
## 74 membrane organization
## 75 cell motility
## 76 system development
## 77 regulation of response to external stimulus
## 78 regulation of multicellular organismal process
## 79 regulation of anatomical structure morphogenesis
## 80 inflammatory response
## 81 regulation of leukocyte mediated immunity
## 82 multicellular organismal process
## 83 positive regulation of response to external stimulus
## 84 locomotion
## 85 positive regulation of multicellular organismal process
## 86 cell adhesion
## 87 cellular developmental process
## 88 regulation of immune effector process
## 89 transport
## 90 cell differentiation
## 91 establishment of localization
## 92 positive regulation of defense response
## 93 hematopoietic or lymphoid organ development
## 94 cellular process
## 95 leukocyte migration
## 96 positive regulation of immune effector process
## 97 animal organ development
## 98 hemopoiesis
## 99 anatomical structure development
## 100 regulation of developmental process
## 101 cell killing
## 102 immune system development
## 103 myeloid leukocyte activation
## 104 leukocyte chemotaxis
## 105 regulation of defense response
## 106 anatomical structure morphogenesis
## 107 multicellular organism development
## 108 response to chemical
## 109 positive regulation of signal transduction
## 110 cell chemotaxis
## 111 myeloid leukocyte migration
## 112 positive regulation of cell communication
## 113 chemotaxis
## 114 taxis
## 115 leukocyte differentiation
## 116 positive regulation of signaling
## 117 intracellular signal transduction
## 118 regulation of signal transduction
## 119 cytokine production
## 120 response to organic substance
## 121 innate immune response activating cell surface receptor signaling pathway
## 122 cellular component organization
## 123 stimulatory C-type lectin receptor signaling pathway
## 124 cellular response to lectin
## 125 response to lectin
## 126 developmental process
## 127 leukocyte degranulation
## 128 regulation of cell killing
## 129 leukocyte mediated cytotoxicity
## 130 innate immune response-activating signal transduction
## 131 regulation of angiogenesis
## 132 regulation of cytokine production
## 133 regulation of vasculature development
## 134 localization
## 135 positive regulation of cell death
## 136 cellular response to chemical stimulus
## 137 angiogenesis
## 138 regulation of leukocyte degranulation
## 139 regulation of signaling
## 140 leukocyte activation involved in immune response
## 141 cell-cell adhesion
## 142 regulation of cell adhesion
## 143 regulation of cell communication
## 144 blood vessel morphogenesis
## 145 cell activation involved in immune response
## 146 cellular component organization or biogenesis
## 147 regulation of natural killer cell mediated immunity
## 148 homeostatic process
## 149 regulation of cell migration
## 150 regulation of leukocyte mediated cytotoxicity
## 151 myeloid leukocyte mediated immunity
## 152 regulation of locomotion
## 153 regulation of natural killer cell mediated cytotoxicity
## 154 response to interferon-gamma
## 155 leukocyte proliferation
## 156 granulocyte migration
## 157 blood vessel development
## 158 regulation of cell motility
## 159 positive regulation of cell killing
## 160 regulation of leukocyte proliferation
## 161 positive regulation of cell adhesion
## 162 cell population proliferation
## 163 natural killer cell mediated immunity
## 164 regulation of biological quality
## 165 positive regulation of leukocyte mediated immunity
## 166 positive regulation of hydrolase activity
## 167 vasculature development
## 168 G protein-coupled receptor signaling pathway
## 169 mononuclear cell migration
## 170 positive regulation of programmed cell death
## 171 regulation of cell death
## 172 positive regulation of cytokine production
## 173 mononuclear cell differentiation
## 174 lymphocyte proliferation
## 175 cell morphogenesis
## 176 natural killer cell mediated cytotoxicity
## 177 positive regulation of intracellular signal transduction
## 178 tube morphogenesis
## 179 positive regulation of response to biotic stimulus
## 180 myeloid cell activation involved in immune response
## 181 mononuclear cell proliferation
## 182 positive regulation of natural killer cell mediated immunity
## 183 regulation of hydrolase activity
## 184 neutrophil chemotaxis
## 185 myeloid cell differentiation
## 186 inorganic ion homeostasis
## 187 neutrophil migration
## 188 cell death
## 189 regulation of response to biotic stimulus
## 190 regulation of programmed cell death
## 191 cation homeostasis
## 192 granulocyte chemotaxis
## 193 response to lipopolysaccharide
## 194 ion homeostasis
## 195 granulocyte activation
## 196 regulation of lymphocyte proliferation
## 197 response to molecule of bacterial origin
## 198 positive regulation of developmental process
## 199 wound healing
## 200 regulation of lymphocyte mediated immunity
## 201 regulation of intracellular signal transduction
## 202 leukocyte cell-cell adhesion
## 203 response to cytokine
## 204 cellular ion homeostasis
## 205 metal ion homeostasis
## 206 MAPK cascade
## 207 regulation of mononuclear cell proliferation
## 208 response to wounding
## 209 regulation of multicellular organismal development
## 210 positive regulation of cell migration
## 211 programmed cell death
## 212 calcium-mediated signaling
## 213 positive regulation of natural killer cell mediated cytotoxicity
## 214 regulation of myeloid leukocyte mediated immunity
## 215 T cell activation
## 216 regulation of inositol phosphate biosynthetic process
## 217 cellular response to organic substance
## 218 positive regulation of molecular function
## 219 positive regulation of cytosolic calcium ion concentration
## 220 circulatory system development
## 221 cellular cation homeostasis
## 222 positive regulation of apoptotic process
## 223 positive regulation of innate immune response
## 224 positive regulation of cell motility
## 225 myeloid leukocyte differentiation
## 226 regulation of MAPK cascade
## 227 regulation of innate immune response
## 228 positive regulation of vasculature development
## 229 positive regulation of angiogenesis
## 230 positive regulation of cell-cell adhesion
## 231 secretion
## 232 cellular metal ion homeostasis
## 233 regulation of cell-cell adhesion
## 234 neutrophil activation
## 235 regulation of cell population proliferation
## 236 tube development
## 237 second-messenger-mediated signaling
## 238 positive regulation of inositol phosphate biosynthetic process
## 239 negative regulation of immune system process
## 240 regulation of apoptotic process
## 241 regulation of inflammatory response
## 242 positive regulation of locomotion
## 243 positive regulation of leukocyte mediated cytotoxicity
## 244 positive regulation of inflammatory response
## 245 regulation of response to stress
## 246 B cell proliferation
## 247 positive regulation of MAPK cascade
## 248 positive regulation of phosphate metabolic process
## 249 positive regulation of phosphorus metabolic process
## 250 positive regulation of cell differentiation
## 251 regulation of molecular function
## 252 cell development
## 253 anatomical structure formation involved in morphogenesis
## 254 response to lipid
## 255 negative regulation of multicellular organismal process
## 256 homeostasis of number of cells
## 257 activation of innate immune response
## 258 apoptotic process
## 259 regulation of cell differentiation
## 260 platelet degranulation
## 261 positive regulation of leukocyte degranulation
## 262 regulation of T cell activation
## 263 monocyte chemotaxis
## 264 positive regulation of cell population proliferation
## 265 positive regulation of lymphocyte mediated immunity
## 266 homotypic cell-cell adhesion
## 267 divalent inorganic cation homeostasis
## 268 multicellular organismal homeostasis
## 269 chemical homeostasis
## 270 cellular divalent inorganic cation homeostasis
## 271 positive regulation of catalytic activity
## 272 antigen processing and presentation of peptide antigen via MHC class II
## 273 negative regulation of biological process
## 274 positive regulation of leukocyte proliferation
## 275 cellular response to cytokine stimulus
## 276 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
## 277 response to oxygen-containing compound
## 278 antigen processing and presentation of peptide antigen
## 279 regulation of secretion
## 280 antigen processing and presentation of exogenous peptide antigen via MHC class II
## 281 neutrophil activation involved in immune response
## 282 cellular chemical homeostasis
## 283 regulation of leukocyte cell-cell adhesion
## 284 modulation of process of another organism
## 285 lymphocyte differentiation
## 286 cell morphogenesis involved in differentiation
## 287 positive regulation of gene expression
## 288 extracellular space
## 289 extracellular region
## 290 external side of plasma membrane
## 291 plasma membrane
## 292 side of membrane
## 293 cell periphery
## 294 cell surface
## 295 immunoglobulin complex
## 296 immunoglobulin complex, circulating
## 297 membrane
## 298 cellular anatomical entity
## 299 cellular_component
## 300 intrinsic component of plasma membrane
## 301 integral component of plasma membrane
## 302 receptor complex
## 303 intrinsic component of membrane
## 304 integral component of membrane
## 305 plasma membrane region
## 306 MHC class II protein complex
## 307 lysosome
## 308 lytic vacuole
## 309 membrane raft
## 310 membrane microdomain
## 311 immunoglobulin receptor binding
## 312 antigen binding
## 313 signaling receptor binding
## 314 protein binding
## 315 molecular transducer activity
## 316 signaling receptor activity
## 317 transmembrane signaling receptor activity
## 318 MHC protein complex binding
## 319 binding
## 320 immune receptor activity
## 321 molecular_function
## 322 MHC class Ib receptor activity
## 323 MHC class I protein complex binding
## 324 MHC class II protein complex binding
## 325 CCR1 chemokine receptor binding
## 326 Meningitis
## 327 Unusual CNS infection
## 328 Unusual infection by anatomical site
## 329 Vasculitis
## 330 Fever
## 331 Constitutional symptom
## 332 Abnormality of temperature regulation
## 333 Skin rash
## 334 Splenomegaly
## 335 Fatigue
## 336 Spherocytosis
## 337 Abnormality of the spleen
## 338 Abnormal circulating IgA level
## 339 Red eye
## 340 Abnormality of the lymph nodes
## 341 Pain
## 342 Autoimmunity
## 343 Abnormal spleen morphology
## 344 Abnormality of fluid regulation
## 345 Abdominal pain
## 346 Cellulitis
## 347 Decreased circulating IgA level
## 348 Abnormal circulating IgM level
## 349 Decreased circulating total IgM
## 350 Arthritis
## 351 Conjunctivitis
## 352 Autosomal dominant inheritance
## 353 Abnormality of the lymphatic system
## 354 Headache
## 355 Abnormal lung morphology
## 356 Bronchiectasis
## 357 Abnormality of blood and blood-forming tissues
## 358 Agammaglobulinemia
## 359 Lymphadenopathy
## 360 Abnormality of skin physiology
## 361 Inflammatory abnormality of the eye
## 362 Anemia due to reduced life span of red cells
## 363 Hemolytic anemia
## 364 Hematopoietic cell lineage
## 365 Graft-versus-host disease
## 366 Allograft rejection
## 367 Type I diabetes mellitus
## 368 Autoimmune thyroid disease
## 369 Asthma
## 370 KEGG root term
## 371 Chemokine signaling pathway
## 372 Antigen processing and presentation
## 373 Intestinal immune network for IgA production
## 374 Leishmaniasis
## 375 Phagosome
## 376 Cytokine-cytokine receptor interaction
## 377 Natural killer cell mediated cytotoxicity
## 378 Tuberculosis
## 379 B cell receptor signaling pathway
## 380 Viral protein interaction with cytokine and cytokine receptor
## 381 Staphylococcus aureus infection
## 382 Viral myocarditis
## 383 Cell adhesion molecules
## 384 Malaria
## 385 Transcriptional misregulation in cancer
## 386 Toxoplasmosis
## 387 Primary immunodeficiency
## 388 Epstein-Barr virus infection
## 389 Rheumatoid arthritis
## 390 C-type lectin receptor signaling pathway
## 391 African trypanosomiasis
## 392 Osteoclast differentiation
## 393 Inflammatory bowel disease
## 394 Th1 and Th2 cell differentiation
## 395 Ras signaling pathway
## 396 mmu-miR-27b-3p
## 397 Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
## 398 FCGR activation
## 399 Scavenging of heme from plasma
## 400 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
## 401 CD22 mediated BCR regulation
## 402 Binding and Uptake of Ligands by Scavenger Receptors
## 403 Role of LAT2/NTAL/LAB on calcium mobilization
## 404 Role of phospholipids in phagocytosis
## 405 Classical antibody-mediated complement activation
## 406 Cell surface interactions at the vascular wall
## 407 Creation of C4 and C2 activators
## 408 FCERI mediated Ca+2 mobilization
## 409 Initial triggering of complement
## 410 FCERI mediated MAPK activation
## 411 Regulation of Complement cascade
## 412 Complement cascade
## 413 Fcgamma receptor (FCGR) dependent phagocytosis
## 414 Innate Immune System
## 415 Regulation of actin dynamics for phagocytic cup formation
## 416 Signaling by the B Cell Receptor (BCR)
## 417 Immune System
## 418 Hemostasis
## 419 FCERI mediated NF-kB activation
## 420 Fc epsilon receptor (FCERI) signaling
## 421 Adaptive Immune System
## 422 Vesicle-mediated transport
## 423 REACTOME root term
## 424 Neutrophil degranulation
## 425 Erythrocytes take up oxygen and release carbon dioxide
## 426 Class A/1 (Rhodopsin-like receptors)
## 427 Erythrocytes take up carbon dioxide and release oxygen
## 428 O2/CO2 exchange in erythrocytes
## 429 Signaling by GPCR
## 430 GPCR ligand binding
## 431 DAP12 interactions
## 432 Signal Transduction
## 433 Chemokine receptors bind chemokines
## 434 GPCR downstream signalling
## 435 Metal sequestration by antimicrobial proteins
## 436 DAP12 signaling
## 437 Peptide ligand-binding receptors
## 438 Response to metal ions
## 439 Metallothioneins bind metals
## 440 Antimicrobial peptides
## 441 RHOA GTPase cycle
## 442 RHO GTPase cycle
## 443 Factor: PU.1; motif: NNNNYYYACTTCCTCTTTY
## 444 Factor: LF-A1; motif: GGGSTCWR
## 445 Factor: SREBP-1; motif: CACSCCA
## 446 Factor: NMYC; motif: CAYCTG; match class: 1
## 447 Factor: IRF-4; motif: NAAARRGGAASTGARANN
## 448 Factor: NMYC; motif: CAYCTG
## 449 Factor: PU.1; motif: AGGAAG
## 450 Factor: Elf-1; motif: AGGAAG
## 451 Factor: Spi-B; motif: TTCYBC
## 452 Factor: Spi-B; motif: TTCYBC; match class: 1
## 453 Transfac
## 454 Factor: PU.1; motif: WGAGGAAG
## 455 Factor: Pax-4; motif: DTTTTCCACCN
## 456 Factor: Sox-18; motif: CAAWGBB
## 457 Factor: LXR-alpha:RXR-alpha; motif: TGACCTNNAGTRACCYNNN
## 458 Factor: Kid3; motif: CCACN
## 459 Factor: LXR-alpha:RXR-alpha; motif: TGACCTNNAGTRACCYNNN; match class: 1
## 460 Factor: Sox-17; motif: TTGTYY
## 461 Factor: C-Jun; motif: TGACTC
## 462 Factor: Kid3; motif: CCACN; match class: 1
## 463 Factor: TEF-1; motif: GRRATG
## 464 Factor: PU.1; motif: AGGAAG; match class: 1
## 465 Factor: Elf-1; motif: AGGAAG; match class: 1
## 466 Factor: TFII-I; motif: NAGGAAGTGN
## 467 Factor: PARP; motif: TTTCYN
## 468 Factor: SREBP-1; motif: KATCACCCCAC
## 469 Factor: MZF-1; motif: TGGGGAR
## 470 Factor: MEL1; motif: GATGAG
## 471 Factor: GKLF; motif: CCTCCYN; match class: 1
## 472 Factor: Lyl-1; motif: NCAKCTGYTNYCNN
## 473 Factor: Sox-18; motif: CAAWGBB; match class: 1
## 474 Factor: elf5; motif: RGAAGRAGGAAGNRRNN
## 475 Factor: PU.1; motif: ARAAAGRGGAAGTGNN
## 476 Factor: ZIC3; motif: NNNCACAGCAKGNNN
## 477 Factor: PEA3; motif: ACWTCCK
## 478 Factor: GKLF; motif: CCTCCYN
## 479 Factor: CPBP; motif: SNCCCNN
## 480 Factor: RXR-ALPHA; motif: KCNCRWAGKTYRNNNN
## 481 Factor: LEF-1; motif: NCCTTTSWNNTNYN
## 482 Factor: LF-A1; motif: GGGSTCWR; match class: 1
## 483 Factor: myogenin; motif: CAGCTG; match class: 1
## 484 Factor: myogenin; motif: CAGCTG
## 485 Factor: Smad4; motif: NTGTCTGNCACN
## 486 Factor: ZIC3; motif: NNNCACAGCAKGNNN; match class: 1
## 487 Factor: Lyl-1; motif: NCAKCTGYTNYCNN; match class: 1
## 488 Factor: Tbx5; motif: TNAGGTGTKV
## 489 Factor: Tal-1; motif: CAGATGG
## 490 Factor: Pax-5; motif: RRNGRNGCAN
## 491 Factor: AML1; motif: TGTGGT; match class: 1
## 492 Factor: AML1a; motif: TGTGGT; match class: 1
## 493 Factor: AML1; motif: TGTGGT; match class: 1
## 494 Factor: TEF-1; motif: RCATTCCWGSN
## 495 Factor: MZF-1; motif: TGGGGAR; match class: 1
## 496 Factor: GATA-5; motif: TATCTN
## 497 Factor: SMAD3; motif: CAGACAS
## 498 Factor: c-Ets-1; motif: RCAGGAAGTGNNTNS
## 499 Factor: Spi1; motif: NRAAAGAGGAAGTGN
## 500 Factor: Elk-1; motif: GGAAGN
## 501 Factor: GR; motif: NNNNNNCNNTNTGTNCTNN; match class: 1
## 502 Factor: Pax-4; motif: NNNNNYCACCCB
## 503 Factor: JunB; motif: NTGAGTCAY
## 504 Factor: NFATc2; motif: GGAAAA
## 505 Factor: NFATc3; motif: GGAAAA
## 506 Factor: NFATc2; motif: GGAAAA
## 507 Factor: KLF; motif: GGGNGGGG; match class: 1
## 508 Factor: PEBP2beta; motif: TGTGGTY
## 509 Factor: CP2; motif: GCHCDAMCCAG
## 510 Factor: Pax-4; motif: NNNNNYCACCCB; match class: 1
## 511 Factor: AML1; motif: TGTGGT
## 512 Factor: AML1a; motif: TGTGGT
## 513 Factor: AML1; motif: TGTGGT
## 514 Factor: RAR-gamma; motif: RGGTCANNNTGNCCNNNN
## 515 Factor: c-Ets-2; motif: CTTCCTG
## 516 Factor: Elk-1; motif: CTTCCKG
## 517 Factor: SMAD3; motif: TGTCTGTCT
## 518 Factor: SMAD3; motif: TGTCTGTCT; match class: 1
## 519 Factor: Sox-10; motif: NACAAWG
## 520 Factor: MZF-1; motif: KNGNKAGGGGNAA
## 521 Factor: GR; motif: NNNNNNCNNTNTGTNCTNN
## 522 Factor: Smad2; motif: AGACAN; match class: 1
## 523 Factor: MAFB; motif: NTCAGCN
## 524 Factor: SMAD4; motif: GKSRKKCAGMCANCY
## 525 Factor: Ets; motif: ACTTCCTS
## 526 Factor: CPBP; motif: SNCCCNN; match class: 1
## 527 Factor: MAFB; motif: NTCAGCN; match class: 1
## 528 Factor: ESRRA; motif: NKNNAGGGGTCANNNNN
## 529 Factor: p300; motif: NNNGGGAGTNNNNS
## 530 WIKIPATHWAYS
## 531 GPCRs, non-odorant
## 532 GPCRs, class A rhodopsin-like
## 533 Microglia pathogen phagocytosis pathway
## 534 Chemokine signaling pathway
## 535 Lung fibrosis
## 536 Tyrobp causal network in microglia
## 537 Focal adhesion
## 538 Macrophage markers
## 539 IL-3 signaling pathway
## effective_domain_size source_order
## 1 21514 291
## 2 21514 271
## 3 21514 286
## 4 21514 2884
## 5 21514 1027
## 6 21514 15390
## 7 21514 15352
## 8 21514 1087
## 9 21514 2881
## 10 21514 13097
## 11 21514 1073
## 12 21514 1401
## 13 21514 1390
## 14 21514 21964
## 15 21514 1397
## 16 21514 13197
## 17 21514 16036
## 18 21514 12178
## 19 21514 905
## 20 21514 550
## 21 21514 3975
## 22 21514 12763
## 23 21514 3973
## 24 21514 906
## 25 21514 1323
## 26 21514 1093
## 27 21514 15295
## 28 21514 15293
## 29 21514 15350
## 30 21514 14876
## 31 21514 14245
## 32 21514 2847
## 33 21514 1321
## 34 21514 22200
## 35 21514 2846
## 36 21514 2887
## 37 21514 11902
## 38 21514 1333
## 39 21514 3061
## 40 21514 4537
## 41 21514 3984
## 42 21514 15364
## 43 21514 1099
## 44 21514 11523
## 45 21514 15363
## 46 21514 903
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## parents
## 1 CORUM:0000000
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## 28 GO:0002682, GO:0006955, GO:0048583
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## 304 GO:0031224
## 305 GO:0005886, GO:0016020
## 306 GO:0042611
## 307 GO:0000323
## 308 GO:0005773
## 309 GO:0098857
## 310 GO:0016020
## 311 GO:0005102
## 312 GO:0005488
## 313 GO:0005515
## 314 GO:0005488
## 315 GO:0003674
## 316 GO:0060089
## 317 GO:0038023
## 318 GO:0044877
## 319 GO:0003674
## 320 GO:0038023
## 321
## 322 GO:0004888, GO:0140375
## 323 GO:0023023
## 324 GO:0023023
## 325 GO:0048020
## 326 HP:0011450
## 327 HP:0002011, HP:0032158
## 328 HP:0032101
## 329 HP:0033353
## 330 HP:0004370
## 331 HP:0000118
## 332 HP:0012337
## 333 HP:0011123
## 334 HP:0003271, HP:0025408
## 335 HP:0025142
## 336 HP:0004447
## 337 HP:0002012, HP:0100763
## 338 HP:0010701
## 339 HP:0008047
## 340 HP:0100763
## 341 HP:0025142
## 342 HP:0010978
## 343 HP:0001743
## 344 HP:0012337
## 345 HP:0011458, HP:0012531
## 346 HP:0003549
## 347 HP:0004313, HP:0410240
## 348 HP:0010701
## 349 HP:0004313, HP:0410243
## 350 HP:0001367
## 351 HP:0000502, HP:0025337, HP:0100533
## 352 HP:0000005
## 353 HP:0002597, HP:0002715
## 354 HP:0012638
## 355 HP:0012252
## 356 HP:0025426
## 357 HP:0000118
## 358 HP:0004313
## 359 HP:0002733
## 360 HP:0000951
## 361 HP:0012373, HP:0012649
## 362 HP:0001903
## 363 HP:0011895
## 364 KEGG:00000
## 365 KEGG:00000
## 366 KEGG:00000
## 367 KEGG:00000
## 368 KEGG:00000
## 369 KEGG:00000
## 370
## 371 KEGG:00000
## 372 KEGG:00000
## 373 KEGG:00000
## 374 KEGG:00000
## 375 KEGG:00000
## 376 KEGG:00000
## 377 KEGG:00000
## 378 KEGG:00000
## 379 KEGG:00000
## 380 KEGG:00000
## 381 KEGG:00000
## 382 KEGG:00000
## 383 KEGG:00000
## 384 KEGG:00000
## 385 KEGG:00000
## 386 KEGG:00000
## 387 KEGG:00000
## 388 KEGG:00000
## 389 KEGG:00000
## 390 KEGG:00000
## 391 KEGG:00000
## 392 KEGG:00000
## 393 KEGG:00000
## 394 KEGG:00000
## 395 KEGG:00000
## 396 MIRNA:000000
## 397 REAC:R-MMU-983705
## 398 REAC:R-MMU-2029480
## 399 REAC:R-MMU-2173782
## 400 REAC:R-MMU-1280218
## 401 REAC:R-MMU-983705
## 402 REAC:R-MMU-5653656
## 403 REAC:R-MMU-2454202
## 404 REAC:R-MMU-2029480
## 405 REAC:R-MMU-166786
## 406 REAC:R-MMU-109582
## 407 REAC:R-MMU-166663
## 408 REAC:R-MMU-2454202
## 409 REAC:R-MMU-166658
## 410 REAC:R-MMU-2454202
## 411 REAC:R-MMU-166658
## 412 REAC:R-MMU-168249
## 413 REAC:R-MMU-168249
## 414 REAC:R-MMU-168256
## 415 REAC:R-MMU-2029480
## 416 REAC:R-MMU-1280218
## 417 REAC:0000000
## 418 REAC:0000000
## 419 REAC:R-MMU-2454202
## 420 REAC:R-MMU-168249
## 421 REAC:R-MMU-168256
## 422 REAC:0000000
## 423
## 424 REAC:R-MMU-168249
## 425 REAC:R-MMU-1480926
## 426 REAC:R-MMU-500792
## 427 REAC:R-MMU-1480926
## 428 REAC:R-MMU-382551
## 429 REAC:R-MMU-162582
## 430 REAC:R-MMU-372790
## 431 REAC:R-MMU-168249
## 432 REAC:0000000
## 433 REAC:R-MMU-375276
## 434 REAC:R-MMU-372790
## 435 REAC:R-MMU-6803157
## 436 REAC:R-MMU-2172127
## 437 REAC:R-MMU-373076
## 438 REAC:R-MMU-8953897
## 439 REAC:R-MMU-5660526
## 440 REAC:R-MMU-168249
## 441 REAC:R-MMU-9012999
## 442 REAC:R-MMU-194315
## 443 TF:M00000
## 444 TF:M00000
## 445 TF:M00000
## 446 TF:M01808
## 447 TF:M00000
## 448 TF:M00000
## 449 TF:M00000
## 450 TF:M00000
## 451 TF:M00000
## 452 TF:M03851
## 453
## 454 TF:M00000
## 455 TF:M00000
## 456 TF:M00000
## 457 TF:M00000
## 458 TF:M00000
## 459 TF:M07107
## 460 TF:M00000
## 461 TF:M00000
## 462 TF:M01160
## 463 TF:M00000
## 464 TF:M02031
## 465 TF:M01266
## 466 TF:M00000
## 467 TF:M00000
## 468 TF:M00000
## 469 TF:M00000
## 470 TF:M00000
## 471 TF:M01835
## 472 TF:M00000
## 473 TF:M03848
## 474 TF:M00000
## 475 TF:M00000
## 476 TF:M00000
## 477 TF:M00000
## 478 TF:M00000
## 479 TF:M00000
## 480 TF:M00000
## 481 TF:M00000
## 482 TF:M00646
## 483 TF:M02101
## 484 TF:M00000
## 485 TF:M00000
## 486 TF:M02941
## 487 TF:M10285
## 488 TF:M00000
## 489 TF:M00000
## 490 TF:M00000
## 491 TF:M02084
## 492 TF:M00271
## 493 TF:M00751
## 494 TF:M00000
## 495 TF:M01733
## 496 TF:M00000
## 497 TF:M00000
## 498 TF:M00000
## 499 TF:M00000
## 500 TF:M00000
## 501 TF:M00192
## 502 TF:M00000
## 503 TF:M00000
## 504 TF:M00000
## 505 TF:M00000
## 506 TF:M00000
## 507 TF:M07461
## 508 TF:M00000
## 509 TF:M00000
## 510 TF:M00378
## 511 TF:M00000
## 512 TF:M00000
## 513 TF:M00000
## 514 TF:M00000
## 515 TF:M00000
## 516 TF:M00000
## 517 TF:M00000
## 518 TF:M00701
## 519 TF:M00000
## 520 TF:M00000
## 521 TF:M00000
## 522 TF:M03580
## 523 TF:M00000
## 524 TF:M00000
## 525 TF:M00000
## 526 TF:M01822
## 527 TF:M08888
## 528 TF:M00000
## 529 TF:M00000
## 530
## 531 WP:000000
## 532 WP:000000
## 533 WP:000000
## 534 WP:000000
## 535 WP:000000
## 536 WP:000000
## 537 WP:000000
## 538 WP:000000
## 539 WP:000000# what are our outputs
#term size
#query size
#query
#intersection size# plot our results using in built function in g:profiler -> which one is it?
gostplot(gost_results_obj)# what does as_short_link = FALSE do in gost() function?
gost_results_obj <- gost(query = upreg_gene_ids, organism = "mmusculus",exclude_iea = TRUE,correction_method = "g_SCS",custom_bg = all_gene_ids,as_short_link = TRUE )## Detected custom background input, domain scope is set to 'custom'gost_results_obj## [1] "https://biit.cs.ut.ee/gplink/l/cldugrK2Sh"Answer ->
# Filter results table for genesets with between 5-300 genes Can you plot these querys together?
Output the get_version_info() to save the versions of the databases that were used for the analysis!!
Output the sessionInfo() so know what packages we used
sessionInfo()## R version 4.2.1 (2022-06-23 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server x64 (build 17763)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_Zimbabwe.1252 LC_CTYPE=English_Zimbabwe.1252
## [3] LC_MONETARY=English_Zimbabwe.1252 LC_NUMERIC=C
## [5] LC_TIME=English_Zimbabwe.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] gprofiler2_0.2.1 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10
## [5] purrr_0.3.5 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
## [9] ggplot2_3.4.0 tidyverse_1.3.2
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.4 sass_0.4.2 bit64_4.0.5
## [4] vroom_1.6.0 jsonlite_1.8.3 viridisLite_0.4.1
## [7] modelr_0.1.10 bslib_0.4.1 shiny_1.7.3
## [10] assertthat_0.2.1 googlesheets4_1.0.1 cellranger_1.1.0
## [13] yaml_2.3.6 pillar_1.8.1 backports_1.4.1
## [16] glue_1.6.2 digest_0.6.30 promises_1.2.0.1
## [19] rvest_1.0.3 colorspace_2.0-3 htmltools_0.5.3
## [22] httpuv_1.6.6 pkgconfig_2.0.3 broom_1.0.1
## [25] haven_2.5.1 xtable_1.8-4 scales_1.2.1
## [28] later_1.3.0 tzdb_0.3.0 googledrive_2.0.0
## [31] generics_0.1.3 ellipsis_0.3.2 cachem_1.0.6
## [34] withr_2.5.0 lazyeval_0.2.2 cli_3.4.1
## [37] mime_0.12 magrittr_2.0.3 crayon_1.5.2
## [40] readxl_1.4.1 evaluate_0.18 fs_1.5.2
## [43] fansi_1.0.3 xml2_1.3.3 tools_4.2.1
## [46] data.table_1.14.4 hms_1.1.2 gargle_1.2.1
## [49] lifecycle_1.0.3 plotly_4.10.1 munsell_0.5.0
## [52] reprex_2.0.2 compiler_4.2.1 jquerylib_0.1.4
## [55] rlang_1.0.6 grid_4.2.1 RCurl_1.98-1.9
## [58] rstudioapi_0.14 htmlwidgets_1.5.4 crosstalk_1.2.0
## [61] bitops_1.0-7 rmarkdown_2.18 gtable_0.3.1
## [64] DBI_1.1.3 R6_2.5.1 lubridate_1.8.0
## [67] knitr_1.40 fastmap_1.1.0 bit_4.0.4
## [70] utf8_1.2.2 stringi_1.7.8 parallel_4.2.1
## [73] Rcpp_1.0.9 vctrs_0.5.0 dbplyr_2.2.1
## [76] tidyselect_1.2.0 xfun_0.34Now knit your report to get a lovely html file that you can share -> this is good practise as it creates a permanent record of your plots/analysis output and also makes sure your script runs without error from start to finish!